glycine catabolic process

The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid.


regulation of plant-type cell wall cellulose catabolic process

biolink:BiologicalProcess biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:NamedThing biolink:Occurrent biolink:OntologyClass biolink:ThingWithTaxon biolink:PhysicalEssenceOrOccurrent

Any process that modulates the frequency, rate or extent of plant-type cell wall cellulose catabolic process.


alcohol oxidase activity

biolink:MolecularActivity biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:NamedThing biolink:Occurrent biolink:OntologyClass biolink:ThingWithTaxon biolink:PhysicalEssenceOrOccurrent

Catalysis of the reaction: a primary alcohol + O2 = an aldehyde + H2O2.


high-affinity fructose transmembrane transporter activity

Enables the transfer of fructose from one side of a membrane to the other. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.


optic cup morphogenesis involved in camera-type eye development

The invagination of the optic vesicle to form two-walled indentations, the optic cups, that will go on to form the retina. This process begins with the optic vesicle becoming a two-walled structure and its subsequent shape changes. It does not include the fate commitment of cells to become the pigmented retina and the neural retina. An example of this process is found in Mus musculus.


facioacoustic ganglion morphogenesis

The developmental process by which an acoustico-facial VII-VIII ganglion complex is generated and organized.


orcinol metabolic process

The chemical reactions and pathways involving orcinol (5-methyl-1,3-benzenediol), an aromatic compound derived from the fermentation of lichen, and synthesized, probably as a fungicide, by some higher plants.


aflatoxin biosynthetic process

The chemical reactions and pathways resulting in the formation of aflatoxin, a fungal metabolite found as a contaminant in moldy grains that induces liver cancer. Aflatoxin induces a G to T transversion at codon 249 of p53, leading to its inactivation. Aflatoxin is converted to a chemical carcinogen by P450.


protein deglutathionylation

The protein modification process in which a glutathione molecule is removed from a protein amino acid by breaking a disulfide linkage.


2-coumarate reductase activity

Catalysis of the reaction: 3-(2-hydroxyphenyl)propanoate + NAD+ = trans-2-coumarate + H+ + NADH.


pentacyclic triterpenoid catabolic process

The chemical reactions and pathways resulting in the breakdown of pentacyclic triterpenoid compounds, terpenoids with six isoprene units and 5 carbon rings.


L-lysine catabolic process to acetate

The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetate.


response to phylloquinone

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a phylloquinone (vitamin K1) stimulus.


female sex determination

The specification of female sex of an individual organism.


peptidyl-S-geranylgeranyl-L-cysteine biosynthetic process from peptidyl-cysteine

The modification of peptidyl-cysteine to form peptidyl-S-geranylgeranylcysteine; formation of S-geranylgeranyl-L-cysteine may be coupled with subsequent cleavage of a carboxy-terminal tripeptide for the CAAX motif and methyl esterification of the geranylgeranylated cysteine; methyl esterification but not cleavage occurs for the CXC motif. For the type II geranylgeranyltransferase the residue may be found at the first and final positions in the sequence motif C-X-C* or at the final position in the sequence motif C-C*. These motifs are necessary but not sufficient for modification.


aldose-6-phosphate reductase (NADPH) activity

Catalysis of the reaction: D-glucitol 6-phosphate + NADP+ = D-glucose 6-phosphate + H+ + NADPH.


The chemical reactions and pathways involving any 1,2-diacyl-sn-glycero-3-phosphocholine, the compounds most commonly designated lecithin.


positive regulation of cellular response to alcohol

Any process that activates or increases the frequency, rate or extent of cellular response to alcohol.


snRNA transcription by RNA polymerase III

The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter.


regulation of endothelial cell differentiation

Any process that modulates the frequency, rate or extent of endothelial cell differentiation.


myrcene synthase activity

Catalysis of the reaction: geranyl diphosphate = diphosphate + myrcene.


riboflavin reductase (NADPH) activity

Catalysis of the reaction: reduced riboflavin + NADP+ = riboflavin + NADPH + 2 H+.


regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching

Any process that modulates the frequency, rate or extent of vascular smooth muscle cell differentiation involved in phenotypic switching.


Catalysis of the reaction: D-glutamate + H2O + O2 = 2-oxoglutarate + NH3 + H2O2, and D-aspartate + H2O + O2 = oxaloacetate + NH3 + H2O2.


D-glutaminase activity

Catalysis of the reaction: H2O + L-glutamine = NH3 + D-glutamate.


methylenetetrahydrofolate reductase NADPH activity

Catalysis of the reaction: 5-methyltetrahydrofolate + NADP + = 5,10-methylenetetrahydrofolate + NADPH + H+.


molybdenum incorporation via L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)

The incorporation of molybdenum into a protein via L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide).


dUDP metabolic process

The chemical reactions and pathways involving dUDP, deoxyuridine (5'-)diphosphate.


G protein-coupled glutamate receptor signaling pathway

biolink:Pathway biolink:BiologicalProcess biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:NamedThing biolink:OntologyClass biolink:Occurrent biolink:ThingWithTaxon biolink:PhysicalEssenceOrOccurrent

A G protein-coupled receptor signaling pathway initiated by glutamate binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process.


DNA repair-dependent chromatin remodeling

A chromatin remodeling process that allows DNA repair enzyme to access genomic DNA and repair DNA lesions.


ectoderm and mesoderm interaction

A cell-cell signaling process occurring between the two gastrulation-generated layers of the ectoderm and the mesoderm.


monoatomic ion homeostasis

Any process involved in the maintenance of an internal steady state of monoatomic ions within an organism or cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.


histone H3K9me/H3K9me2 demethylase activity

Catalysis of the removal of a methyl group from a di or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.


T-helper 1 cell activation

The change in morphology and behavior of a T-helper 1 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.


positive regulation of systemic arterial blood pressure

The process that increases the force with which blood travels through the systemic arterial circulatory system.


Catalysis of the reaction: L-2,4-diaminobutyrate + pyruvate = L-alanine + L-aspartate 4-semialdehyde.


response to L-dopa

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-dopa stimulus.


dermatan sulfate metabolic process

The chemical reactions and pathways involving dermatan sulfate, any of a group of glycosaminoglycans with repeats consisting of beta-(1,4)-linked L-iduronyl-beta-(1,3)-N-acetyl-D-galactosamine 4-sulfate units. They are important components of ground substance or intercellular cement of skin and some connective tissues.


deoxycytidine metabolic process

The chemical reactions and pathways involving deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA.


regulation of SREBP signaling pathway

Any process that modulates the frequency, rate or extent of the SREBP signaling pathway.


positive regulation of endothelial cell-matrix adhesion via fibronectin

Any process that activates or increases the frequency, rate or extent of endothelial cell-matrix adhesion via fibronectin.


Catalysis of the reaction: glucomannan(n) + GDP-mannose = glucomannan(n+1) + GDP.


IDP phosphatase activity

Catalysis of the reaction: IDP + H2O = IMP + H+ + phosphate.


pollen adhesion

The process in which pollen deposited on the stigma adheres to cells of the stigma.


distal tubule morphogenesis

The process in which the anatomical structures of a distal tubule are generated and organized. The distal tubule is a nephron tubule that begins at the macula densa and extends to the connecting tubule.


response to phorbol 13-acetate 12-myristate

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a phorbol 13-acetate 12-myristate stimulus.


maleylacetoacetate isomerase activity

Catalysis of the reaction: 4-maleylacetoacetate = 4-fumarylacetoacetate.


nephric duct development

The process whose specific outcome is the progression of a nephric duct over time, from its initial formation to a mature structure. A nephric duct is a tube that drains a primitive kidney.


L-isoleucine transaminase activity

Catalysis of the reaction: 2-oxoglutarate + L-isoleucine = (S)-3-methyl-2-oxopentanoic acid + L-glutamic acid.


regulation of rhamnose catabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.


regulation of filamentous growth of a population of unicellular organisms in response to heat

Any process that modulates the frequency, rate or extent of filamentous growth of a population of unicellular organisms in response to heat.


regulation of wound healing, spreading of epidermal cells

Any process that modulates the frequency, rate or extent of wound healing, spreading of epidermal cells.


negative regulation of embryonic pattern specification

Any process that stops, prevents or reduces the frequency, rate or extent of embryonic pattern specification.


follicular dendritic cell differentiation

The process in which a relatively unspecialized precursor cell acquires the specialized features of a follicular dendritic cell.


pro-T cell differentiation

The process in which a precursor cell type acquires the specialized features of a pro-T cell. Pro-T cells are the earliest stage of the T cell lineage but are not fully committed.


endothelial cell chemotaxis to fibroblast growth factor

The directed movement of an endothelial cell in response to the presence of fibroblast growth factor (FGF).


prostaglandin production involved in inflammatory response

The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.


D-xylose 1-dehydrogenase (NADP+) activity

Catalysis of the reaction: D-xylose + NADP+ = D-xylono-1,5-lactone + H+ + NADPH.


regulation of glial cell differentiation

Any process that modulates the frequency, rate or extent of glia cell differentiation.


Catalysis of the reaction: L-seryl-[protein] + NAD+ = H+ + nicotinamide + O-(ADP-D-ribosyl)-L-seryl-[protein].


Catalysis of the reaction: (1->6)-alpha-D-mannosyloligosaccharide + beta-D-mannosylphosphodecaprenol = (1->6)-alpha-D-mannosyl-(1->6)-alpha-D-mannosyl-oligosaccharide + decaprenol phosphate.


negative regulation of cell motility involved in cerebral cortex radial glia guided migration

The intracellular signaling pathway that results in the cessation of cell movement involved in lamination of the cerebral cortex.


regulation of oligopeptide transport

Any process that modulates the frequency, rate or extent of the directed movement of oligopeptides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages.


green leaf volatile biosynthetic process

The chemical reactions and pathways resulting in the formation of volatile molecules emitted from green plants, such as hexenal, hexenol and hexenyl acetate, from linoleic acid or linolenic acid.


negative regulation of lens fiber cell differentiation

Any process that stops, prevents or reduces the frequency, rate or extent of lens fiber cell differentiation.


2-methylguanosine metabolic process

The chemical reactions and pathways involving 2-methylguanosine.


phenylacetaldehyde synthase activity

Catalyzes the reaction: L-phenylalanine + O2 + H2O -> phenylacetaldehyde + ammonia + hydrogen peroxide + CO2.


apoptotic process involved in mammary gland involution

Any apoptotic process that triggers the activity of proteolytic caspases whose actions dismantle the mammary epithelial cells resulting in their programmed cell death.


protoperithecium formation

The process of producing fruiting body precursors, called protoperithecia. Protoperitheicium is a spherical structure that is formed in the sexual phase of ascomycetous fungi such as Neurospora crassa and Sordaria macrospora. Protoperithecium is formed by the enveloping of ascogonia cells by sterile hyphae and it develops into perithecium.


regulation of dense core granule transport

Any process that modulates the frequency, rate or extent of dense core granule transport.


Notch signaling pathway involved in arterial endothelial cell fate commitment

The series of molecular signals initiated by binding of an extracellular ligand to a Notch receptor on the surface of the target cell and contributing to the commitment of a cell to an arterial endothelial cell fate.


molybdenum incorporation via L-cysteinyl molybdopterin

The incorporation of molybdenum into a protein via L-cysteinyl molybdopterin.


Catalysis of the reaction: 1-18:3-2-16:0-phosphatidylglycerol + O2 + a reduced electron acceptor <=> 1-18:3-2-trans-16:1-phosphatidylglycerol + 2 H2O + an oxidized electron acceptor.


Catalysis of the reaction: N(4)-(beta-N-acetyl-D-glucosaminyl)-L-asparagine + H2O = N-acetyl-D-glucosamine + L-asparagine.


establishment of protein localization to plasma membrane

The directed movement of a protein to a specific location in a plasma membrane.


trihydroxyferuloyl spermidine:S-adenosyl-L-methionine O-methyltransferase activity

Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the oxygen atom of a trihydroxyferuloyl spermidine molecule.


beta-1,3-galactosyltransferase activity

Catalysis of the transfer of a galactose residue from a donor molecule to an oligosaccharide, forming a beta-1,3-linkage.


positive regulation of T cell differentiation in thymus

Any process that activates or increases the frequency, rate or extent of T cell differentiation in the thymus.


histoblast morphogenesis

The process in which the anatomical structures derived from the histoblast disc are generated and organized. This includes the transformation of histoblast cells into adult structures during pupal metamorphosis. Histoblast cells are cells founded in the embryo that are the progenitors to the adult abdomen.


response to redox state

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.


positive regulation of fat cell proliferation

Any process that activates or increases the rate or extent of fat cell proliferation.


oxidoreductase activity, acting on other nitrogenous compounds as donors

Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.


anaerobic respiration

The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.


mono-butyltin dioxygenase activity

Catalysis of the reaction: butyltin + O2 + 2 H+ + 2 e- = H2O + beta-hydroxybutyltin.


regulation of macrophage activation

Any process that modulates the frequency or rate of macrophage activation.


mesenchyme migration

The process in which the population of cells that make up a mesenchyme undergo directed movement.


positive regulation of erythrocyte clearance

Any process that activates or increases the frequency, rate, or extent of erythrocyte clearance.


renal system pattern specification

Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate into the anatomical structures of the renal system.


embryonic heart tube morphogenesis

The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.


isopentenyl diphosphate biosynthetic process

The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids.


cotranslational protein targeting to membrane

The targeting of proteins to a membrane that occurs during translation. The transport of most secretory proteins, particularly those with more than 100 amino acids, into the endoplasmic reticulum lumen occurs in this manner, as does the import of some proteins into mitochondria.


2,3-dimethylmalate lyase activity

Catalysis of the reaction: (2R,3S)-2,3-dimethylmalate = propanoate + pyruvate.


reproductive process

A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.


lysine biosynthetic process via diaminopimelate, dehydrogenase pathway

The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in a single enzymatic step.


voltage-gated sodium channel activity involved in cardiac muscle cell action potential

Enables the transmembrane transfer of a sodium ion by a voltage-gated channel through the plasma membrane of a cardiac muscle cell contributing to the depolarization phase of an action potential. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.


positive regulation of cholesterol transport

Any process that activates or increases the frequency, rate or extent of the directed movement of cholesterol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


Catalysis of the reaction: NAD(P)+ + L-serine = nicotinamide + N2-(ADP-D-ribosyl)-L-serine.


negative regulation of pole plasm oskar mRNA localization

Any process that stops, prevents, or reduces the frequency, rate or extent of a process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm.


response to peptidoglycan

Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptidoglycan stimulus. Peptidoglycan is a bacterial cell wall macromolecule.


T cell differentiation involved in immune response

The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells.


positive regulation of maltohexaose transport

Any process that activates or increases the frequency, rate or extent of maltohexaose transport.


negative regulation of ATP-dependent activity

Any process that stops or reduces the rate of an ATP-dependent activity.


regulation of mitotic telomere tethering at nuclear periphery

Any process that modulates the frequency, rate or extent of mitotic telomere tethering at nuclear periphery.


actin filament bundle retrograde transport

A process of actin filament bundle distribution that results in the arrangement of actin filament bundles from the periphery toward the interior of the cell.


fibroblast chemotaxis

The directed movement of a fibroblast guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).


positive regulation of leukocyte cell-cell adhesion

Any process that activates or increases the frequency, rate or extent of leukocyte cell-cell adhesion.


G protein-coupled purinergic nucleotide receptor activity

Combining with a purine nucleotide and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.


[heparan sulfate]-glucosamine N-sulfotransferase activity

Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-N-sulfoglucosamine.


tRNA wobble base modification

The process in which the nucleotide at position 34 in the anticodon of a tRNA is post-transcriptionally modified.


L-kynurenine catabolic process

The chemical reactions and pathways resulting in the breakdown of L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine).


flavin-dependent halogenase activity

Catalysis of the reaction: R-CH + a halogen + FADH2 + O2 = R-C-halogen + FAD + H2O.


oleate transmembrane transporter activity

Enables the transfer of oleate from one side of a membrane to the other.


Catalysis of the reaction: CMP-N-acetylneuraminate + glycano-(1->3)-(N-acetyl-alpha-D-galactosaminyl)-glycoprotein = CMP + glycano-[(2->6)-alpha-N-acetylneuraminyl]-(N-acetyl-D-galactosaminyl)-glycoprotein.


positive regulation of lactation by mesenchymal-epithelial cell signaling

The process that increases the rate, frequency, or extent of lactation as a result of the secretion of a signal from the mammary fat and its reception by a mammary epithelial cell.


positive regulation of SREBP signaling pathway in response to decreased oxygen levels

Any process that activates or increases the frequency, rate or extent of the SREBP signaling pathway in response to a decrease in oxygen levels.


delamination involved in gastrulation with mouth forming second

The splitting or migration of one epithelial sheet into two involved in the process of deuterostomic gastrulation.


response to oxygen levels

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen.


procyclogenesis

The morphological, biochemical and genetic changes that induce the differentiation of bloodstream form trypomastigotes into procyclic trypomastigotes in some of the Trypanosomatidae species such as Trypanosoma brucei. This process occurs inside the midgut of the tsetse fly vectors in T. brucei.


fibroblast growth factor receptor signaling pathway involved in spinal cord anterior/posterior pattern formation

The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands that results in the spatial identity of regions along the anterior-posterior axis of the spinal cord.


cytochrome P450 dependent beta-amyrin 12,13beta-epoxidase activity

Catalysis of the reaction: beta-amyrin + O2 + H+ + NAD(P)H <=> 12,13beta-epoxy-beta-amyrin + H2O + NAD(P).


peptidyl-proline hydroxylation

The hydroxylation of peptidyl-proline to form peptidyl-hydroxyproline.


positive regulation of sensory perception of bitter taste

Any process that activates or increases the frequency, rate or extent of sensory perception of bitter taste.


mannosamine biosynthetic process

The chemical reactions and pathways resulting in the formation of mannosomine, 2-amino-2-deoxymannose; the D-isomer is a constituent of neuraminic acids as well as mucolipids and mucoproteins.


acetylornithine deacetylase activity

Catalysis of the reaction: N2-acetyl-L-ornithine + H2O = acetate + L-ornithine.


small RNA binding translational repressor activity

A translational repressor activity that binds to a single-stranded small regulatory RNA (either a miRNA or a siRNA) to guide it to its target mRNA.


wobble position uridine ribose methylation

The process in which the ribose of uridine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position.


histone H2A methyltransferase activity

Catalysis of the reaction: S-adenosyl-L-methionine + a histone H2 = S-adenosyl-L-homocysteine + a methylated histone H2A. Histone methylation generally occurs on either an arginine or a lysine residue.


N-glutamylanilide hydrolase activity

Catalysis of the reaction: N5-phenyl-L-glutamine + H2O = L-glutamate + aniline + H+.


positive regulation of colon smooth muscle contraction

Any process that activates or increases the frequency, rate or extent of colon smooth muscle contraction.


kaempferol O-glucoside biosynthetic process

The chemical reactions and pathways leading to the formation of O-glucosylated derivatives of kaempferol.


The series of molecular signals initiated by thrombopoietin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


renal capsule morphogenesis

The process in which the anatomical structures of the renal capsule are generated and organized. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands.


protein urmylation

Covalent attachment of the ubiquitin-like protein URM1 to another protein.


lobar bronchus mesenchyme development

The biological process whose specific outcome is the progression of a lobar bronchus mesenchyme from an initial condition to its mature state. This process begins with the formation of the lobar bronchus mesenchyme and ends with the mature structure. The lobar bronchus mesenchyme is the mass of tissue composed of mesenchymal cells in the lobar bronchus.


alpha1-adrenergic receptor activity

Combining with epinephrine or norepinephrine to initiate a change in cell activity via activation of a G protein, with pharmacological characteristics of alpha1-adrenergic receptors; the activity involves transmitting the signal to the Gq alpha subunit of a heterotrimeric G protein.


amylase activity

Catalysis of the hydrolysis of amylose or an amylose derivative.


(25S)-Delta(7)-dafachronate binding

Binding to (25S)-Delta(7)-dafachronate.


Catalysis of the reaction: 2-oxo-7-methylthioheptanoate + acetyl-CoA + H2O <=> H+ + 2-(5'-methylthio)pentylmalate + coenzyme A.


synaptic transmission, GABAergic

The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.


regulation of DNA topoisomerase (ATP-hydrolyzing) activity

Any process that modulates the frequency, rate or extent of DNA topoisomerase (ATP-hydrolyzing) activity.


negative regulation of osteoblast differentiation

Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.


NAD+ synthase activity

Catalysis of the reaction: ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+.


negative regulation of response to acetate

Any process that stops, prevents or reduces the frequency, rate or extent of response to acetate.


stomatal complex development

The process whose specific outcome is the progression of the stomatal complex over time from its formation to the mature structure. The stomatal complex is the stomatal guard cells and their associated epidermal cells.


antisense RNA metabolic process

The chemical reactions and pathways involving antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis.


regulation of endothelial tube morphogenesis

Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis.


menaquinone-dependent protoporphyrinogen oxidase activity

Catalysis of the reaction: protoporphyrinogen IX + menaquinone = protoporphyrin IX + reduced menaquinone.


olfactory nerve structural organization

The process that contributes to the act of creating the structural organization of the oculomotor nerve. This process pertains to the physical shaping of a rudimentary structure. The olfactory nerve is a collection of sensory nerve rootlets that extend down from the olfactory bulb to the olfactory mucosa of the upper parts of the nasal cavity. This nerve conducts odor information to the brainstem.


corticospinal neuron axon guidance

The process in which the migration of an axon growth cone of a neuron that is part of the corticospinal tract is directed from the cerebral cortex layer V to the spinal cord dorsal funiculus in response to a combination of attractive and repulsive cues.


pentose catabolic process to acetate

The chemical reactions and pathways resulting in the breakdown of pentose to acetate.


regulation of retinal cone cell fate specification

Any process that mediates the specification of a cell into a retinal cone cell.


monocarboxylic acid binding

Binding to a monocarboxylic acid, any organic acid containing one carboxyl (COOH) group or anion (COO-).


regulation of neuronal action potential

Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a neuron. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.


leptin receptor activity

Combining with the fat-cell specific hormone leptin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.


20-hydroxy-leukotriene B4 omega oxidase activity

Catalysis of the reaction: 20-hydroxy-leukotriene B4 + O2 + reduced [NADPH-hemoprotein reductase] = 20-oxo-leukotriene B4 + H+ + 2 H2O + oxidized [NADPH-hemoprotein reductase].


tergite morphogenesis

The process in which the anatomical structures of the tergite are generated and organized. The tergite is the primary plate or sclerite forming the dorsal surface of any insect body segment.


long-chain fatty acid metabolic process

The chemical reactions and pathways involving a long-chain fatty acid, a fatty acid with an aliphatic tail of 13 to 21 carbons.


chromosome, subtelomeric region

biolink:CellularComponent biolink:AnatomicalEntity biolink:OrganismalEntity biolink:BiologicalEntity biolink:NamedThing biolink:PhysicalEssence biolink:SubjectOfInvestigation biolink:ThingWithTaxon biolink:PhysicalEssenceOrOccurrent

A region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes. This region is usually heterochromatin.


chromosomal region

Any subdivision of a chromosome along its length.


chromosome, telomeric region

The end of a linear chromosome, required for the integrity and maintenance of the end. A chromosome telomere usually includes a region of telomerase-encoded repeats the length of which rarely exceeds 20 bp each and that permits the formation of a telomeric loop (T-loop). The telomeric repeat region is usually preceded by a sub-telomeric region that is gene-poor but rich in repetitive elements. Some telomeres only consist of the latter part (for eg. D. melanogaster telomeres).


polytene chromosome puff

A swelling at a site along the length of a polytene chromosome, thought to be the site of active transcription.


chromosome, telomeric repeat region

A complex of DNA and protein that seals the end of a chromosome. The telomeric repeat DNA consists of simple tandemly repeated sequences specific for each species. Typically one strand is G-rich and the other C-rich. The G-rich strand forms a 3'-terminal overhang, the length of which varies with species. The single strand overhang is bound by a variety of proteins, including telomere capping proteins that bind to the single-stranded DNA and seal the telomeric loop.


polytene chromosome band

A stretch of densely packed chromatin along the polytene chromosome, visible as a morphologically distinct band.


condensed chromosome, centromeric region

The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.


polytene chromosome interband

A stretch of less tightly packed chromatin along the polytene chromosome, found between bands.


chromosome, centromeric region

The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.


chromosome, centromeric core domain

The innermost portion of the centromeric region of a chromosome, encompassing the core region of a chromosome centromere and the proteins that bind to it.


DNA topoisomerase III-beta-TDRD3 complex

A protein complex that has DNA topoisomerase type I and RNA topoisomerase activities.


host bacteroid-containing symbiosome

A symbiosome containing any of various structurally modified bacteria, such as those occurring on the root nodules of leguminous plants, of a host cell.


growth hormone receptor complex

A receptor complex that consists of two identical subunits and binds growth hormone.


APC-tubulin-IQGAP1 complex

A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), alpha-tubulin, gamma-tubulin, and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization.


simple sieve plate

A sieve plate that contains a single specialized sieve area.


sieve plate

A part of the cell wall of a sieve tube member that bears one or more highly specialized sieve areas.


compound sieve plate

A sieve plate that contains several specialized sieve areas in either a scalariform or reticulate arrangement.


Cdc48p-Npl4p-Vms1p AAA ATPase complex

A multiprotein ATPase complex involved in the release of polyubiquitinated proteins, including those damaged by oxidative stress, from the outer mitochondria membrane into the cytoplasm where they are presented to the proteasome for proteolysis, a process also referred to as mitochondria-associated degradation (MAD). In budding yeast, this complex includes Cdc48p, Npl4p and Vms1p.


mRNA cleavage factor complex

Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.


mRNA cleavage stimulating factor complex

A protein complex required for mRNA cleavage but not for poly(A) addition.


mRNA cleavage and polyadenylation specificity factor complex

A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal.


meiotic nuclear membrane microtubule tethering complex

A nuclear membrane protein complex which connects the nuclear outer and inner membranes together, and links links the nuclear lumen to cytoplasmic microtubules during meiosis.


Sad1-Kms1 LINC complex

A LINC complex implicated in the connection of DNA double strand breaks to the cytoskeleton during DNA double-strand break repair.


interleukin-15 receptor complex

A protein complex that binds interleukin-15 (IL-15) and that consists of, at a minimum, an interleukin, an alpha, beta and gamma chain as well as optional additional kinase subunits. The alpha chain is unique to binds IL-15 while it shares the beta chain with the IL-2 receptor and the cytokine receptor common gamma chain with multiple interleukin receptors.


alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex

A catalytic protein complex that is capable of alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity.


cytoproct

Stable, specialized structure for extrusion of waste by the cell into the surrounding medium.


activin A complex

A nonsteroidal regulator, composed of two covalently linked inhibin beta-A subunits (sometimes known as activin beta-A or activin/inhibin beta-A).


activin complex

A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits, inhibin beta-A and inhibin beta-B (sometimes known as activin beta or activin/inhibin beta). There are three forms of activin complex, activin A, which is composed of 2 inhibin beta-A subunits, activin B, which is composed of 2 inhibin beta-B subunits, and activin AB, which is composed of an inhibin beta-A and an inhibin beta-B subunit.


activin AB complex

A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits (sometimes known as activin beta or activin/inhibin beta), inhibin beta-A and inhibin beta-B.


activin B complex

A nonsteroidal regulator, composed of two covalently linked inhibin beta-B subunits (sometimes known as activin beta-B or activin/inhibin beta-B).


hippocampal mossy fiber expansion

Synaptic expansion of hippocampal mossy fiber axon that makes contact with the thorny excrescences of hippocampal CA3 pyramidal cell dendrites.


alphaV-beta3 integrin-tissue transglutaminase complex

A protein complex that consists of an alphaV-beta3 integrin complex bound to tissue transglutaminase.


vacuole-isolation membrane contact site

An organelle membrane contact site formed at the junction of the vacuolar membrane and the isolation membrane or phagophore in response to starvation or other stresses, leading to the formation of the autophagosome.


organelle membrane contact site

A zone of apposition between the membranes of an organelle with another membrane, either another membrane of the same organelle, a membrane of another organelle, or the plasma membrane. Membrane contact sites (MCSs) are structured by bridging complexes. They are specialized for communication, including the efficient traffic of small molecules such as Ca2+ ions and lipids, as well as enzyme-substrate interactions.


endoplasmic reticulum-endosome membrane contact site

A contact site between the endoplasmic reticulum membrane and the endosome membrane.


endoplasmic reticulum-vacuole membrane contact site

A zone of apposition between endoplasmic-reticulum and lytic vacuole membranes, structured by bridging complexes.


vacuole-mitochondrion membrane contact site

A zone of apposition between the vacuolar membrane and the mitochondrial outer membrane, important for transfer of lipids between the two organelles.


mitochondrial crista junction

A tubular structure of relatively uniform size that connects a mitochondrial crista to the mitochondrial inner boundary membrane.


mitochondrial inner-outer membrane contact site

Sites of close apposition of the inner and outer mitochondrial membrane.


nucleus-vacuole junction

An organelle membrane contact site formed between the vacuole membrane and the outer nuclear membrane. In S. cerevisiae these contacts are mediated through direct physical interaction between Vac8p and Nvj1p.


endoplasmic reticulum-plasma membrane contact site

A contact site between the endoplasmic reticulum membrane and the plasma membrane, structured by bridging complexes.


mitochondria-associated endoplasmic reticulum membrane

A zone of apposition between endoplasmic-reticulum and mitochondrial membranes, structured by bridging complexes. These contact sites are thought to facilitate inter-organelle calcium and phospholipid exchange.


ribonucleoprotein granule

A non-membranous macromolecular complex containing proteins and translationally silenced mRNAs. RNA granules contain proteins that control the localization, stability, and translation of their RNA cargo. Different types of RNA granules (RGs) exist, depending on the cell type and cellular conditions.


Z granule

A small cytoplasmic, non-membranous RNA/protein complex aggregate in the primordial germ cells that are distinct from, but colocalize with or are adjacent to, P granules and mutator foci and are associated with RNA metabolism. Z granules have been observed in C. elegans.


pi-body

A P granule that contains the PIWIL2-TDRD1 module, a set of proteins that act in the primary piRNA pathway. The pi-body corresponds to the cementing material between mitochondria found in gonocytes.


cytoplasmic ribonucleoprotein granule

A ribonucleoprotein granule located in the cytoplasm.


TIS granule

A ribonucleoprotein granule located in the cytoplasm that is formed by the RNA-binding protein TIS11B and RNA molecules, enriched in membrane protein-encoding mRNAs with multiple AU-rich elements. TIS granules are reticular meshworks intertwined with the endoplasmic reticulum (ER).


GW body

A ribonucleoprotein granule located in the cytoplasm and the nucleus. GW-bodies minimally contain the Argonaute2 (Ago2) and TNRC6B proteins, together with specific target RNAs.


piP-body

A P granule that contains the PIWIL4-TDRD9 module, a set of proteins that act in the secondary piRNA pathway.


RNP body

A ribonucleoprotein granule located in the cytoplasm of bacteria, minimally containing the RNase E protein and RNA molecules. Bacterial RNP-bodies are similar to eukaryotic P-bodies and stress granules.


nuclear stress granule

A dense aggregation in the nucleus composed of proteins and RNAs that appear when the cell is under stress.


chromatoid body

A ribonucleoprotein complex found in the cytoplasm of male germ cells, composed of exceedingly thin filaments that are consolidated into a compact mass or into dense strands of varying thickness that branch to form an irregular network. Contains mRNAs, miRNAs, and protein components involved in miRNA processing (such as Argonaute proteins and the endonuclease Dicer) and in RNA decay (such as the decapping enzyme DCP1a and GW182).


neuronal ribonucleoprotein granule

A ribonucleoprotein complex that is found in the cytoplasm of axons and dendrites, and transports translationally silenced mRNAs to dendritic synapses, where they are released and translated in response to specific exogenous stimuli.


TRC complex

A protein complex found in yeast that contains GET4, MDY2 (GET5), SGT2, and at least two heat shock proteins, HSP104 and YBR137W. The TRC complex transfers tail-anchored (TA) proteins to GET3 for targeting to the endoplasmic reticulum membrane.


pre-snoRNP complex

A ribonucleoprotein complex that contains a precursor small nucleolar RNA (pre-snoRNA) and associated proteins, and forms during small nucleolar ribonucleoprotein complex (snoRNP) assembly. Pre-snoRNP complexes may contain proteins not found in the corresponding mature snoRNP complexes.


cytoplasmic DNA replication factor C complex

A cytoplasmic complex of two polypeptides that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. Examples of this component are found in prokaryotic species.


nuclear DNA replication factor C complex

A nuclear complex of five polypeptides that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase delta or epsilon. In Saccharomyces and several other species, the subunits are known as Rfc1p-Rfc5p, although subunit names do not necessarily correspond between different species.


DNA polymerase III, beta sliding clamp processivity factor complex

A subcomplex of the DNA polymerase III holoenzyme which is responsible for tethering the catalytic subunit of DNA polymerase to DNA during high-speed replication. The complex is homodimeric in prokaryotes, and homotrimeric in other species.


HU-DNA complex

A protein-DNA complex that consists of HU heterodimers (an alpha and a beta chain) assembled into octamers along DNA. HU binds to double-stranded DNA in a structure- and sequence-specific manner and bends the DNA into a nucleosome-like structure.


DNA bending complex

A protein-DNA complex that contains DNA in combination with a protein which binds to and bends DNA. Often plays a role in DNA compaction.


H-NS complex

A multimer of H-NS proteins that is involved in bacterial nucleoid condensation and negative regulation of global gene expression by directly binding to promoter regions. Recognizes both structural and sequence-specific motifs in double-stranded DNA and has binding preference for bent DNA.


IHF-DNA complex

A protein-DNA complex containing IHF heterodimers (an alpha and a beta chain) bound to DNA. IHF binds to double-stranded DNA in a structure- and sequence-specific manner and bends the DNA into a nucleosome-like structure, the bacterial nucleoid.


extrinsic component of phagophore assembly site membrane

The component of the phagophore assembly site membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of organelle membrane

The component of an organelle membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of postsynaptic early endosome membrane

The component of the postsynaptic early endosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of intraperoxisomal membrane

The component of the intraperoxisomal membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of postsynaptic recycling endosome membrane

The component of the postsynaptic recycling endosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of nuclear outer membrane

The component of a nuclear outer membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of synaptic vesicle membrane

The component of the synaptic vesicle membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of plastid thylakoid membrane

The component of a plastid thylakoid membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of plastid membrane

The component of a plastid membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of stromal side of plastid thylakoid membrane

The component of a plastid thylakoid membrane consisting of gene products and protein complexes that are loosely bound to its stromal surface, but not integrated into the hydrophobic region.


extrinsic component of neuronal dense core vesicle membrane

The component of the neuronal dense core vesicle membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of plastid inner membrane

The component of a plastid inner membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of presynaptic endosome membrane

The component of the presynaptic endosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of omegasome membrane

The component of the omegasome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of mitochondrial outer membrane

The component of a mitochondrial outer membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of postsynaptic endosome membrane

The component of the postsynaptic endosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of Golgi membrane

The component of a Golgi membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of lumenal side of plastid thylakoid membrane

The component of a plastid thylakoid membrane consisting of gene products and protein complexes that are loosely bound to its lumenal surface, but not integrated into the hydrophobic region.


extrinsic component of mitochondrial inner membrane

The component of mitochondrial inner membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of stromal side of plastid inner membrane

The component of a plastid inner membrane consisting of gene products and protein complexes that are loosely bound to its stromal surface, but not integrated into the hydrophobic region.


extrinsic component of endosome membrane

The component of an endosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of matrix side of mitochondrial inner membrane

The component of the matrix side of the mitochondrial inner membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of endoplasmic reticulum membrane

The component of the endoplasmic reticulum membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


extrinsic component of dense core granule membrane

The component of the dense core granule membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


protein C inhibitor-PLAT complex

A heterodimeric protein complex that contains protein C inhibitor (SERPINA5) and tissue-type plasminogen activator (PLAT); formation of the complex inhibits the serine protease activity of tissue-type plasminogen activator.


dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt2p dimer complex

A protein dimer complex that possesses dolichyl-phosphate-mannose-protein mannosyltransferase activity and, in S. cerevisiae, is composed of Pmt1p-Pmt2p.


The region between the inner and outer lipid bilayers of the longitudinal sarcoplasmic reticulum envelope. The longitudinal sarcoplasmic reticulum lumen is continuous with the lumen contained within the terminal cisternae.


deuterosome

A spherical, electron dense, cytoplasmic structure that is involved in de novo assembly of centrioles.


transcription factor TFIIF complex

A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.


bacterial-type flagellum

A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.


periplasmic flagellum

Flagellar filaments located in the periplasmic space; characterized in spirochetes, in which they are essential for shape and motility. Composed of a core surrounded by two sheath layers, the flagella rotate to allow migration of the cell through viscous media, which would not be possible using external flagella.


COPI-coated Golgi to ER transport vesicle

A vesicle that mediates transport from the Golgi to the endoplasmic reticulum.


chromoplast outer membrane

The outer, i.e. cytoplasm-facing, lipid bilayer of the chromoplast envelope.


viral factory

An intracellular compartment in a host cell which increases the efficiency of viral replication, and shields the virus from host defenses. Viral factories can be either cytoplasmic or nuclear and often arise from extensive rearrangement of host cell cytoskeletal and/or cell membrane compartments.


double membrane vesicle viral factory

A cytoplasmic viral factory that consists of a double-membrane bound vesicle. Has a diameter of 200-300nm and is derived from the endoplasmic reticulum or Golgi apparatus. Produced by Picornaviridae, Nidovirales, Arteriviridae and Coronaviridae.


tube viral factory

A cytoplasmic viral factory derived from the Golgi in which Bunyaviridae replication takes place. Tubes are membranous structures close to the assembly and budding sites, and their function may be to connect viral replication and morphogenesis inside viral factories.


viroplasm viral factory

A cytoplasmic viral factory that is electron dense due to high levels of viral RNA. Produced by nucleo-cytoplasmic large DNA viruses (NCLDV) like Poxviridae, Asfarviridae and Iridoviridae, and dsRNA viruses like Reoviridae.


spherule viral factory

A cytoplasmic viral factory which is a 50-400nm diameter membrane invagination. Spherules can appear on several enveloped cellular components depending on the virus.


phosphopyruvate hydratase complex

A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.


phosphoenolpyruvate-dependent sugar phosphotransferase complex

Includes phosphoenolpyruvate-protein phosphatase (enzyme I of the phosphotransferase system) and protein-N(PI)-phosphohistidine-sugar phosphotransferase (enzyme II of the phosphotransferase system).


cytoplasmic microtubule bundle

Any microtubule bundle that is part of a cytoplasm.


microtubule bundle

An arrangement of closely apposed microtubules running parallel to each other.


axon microtubule bundle

An arrangement of closely apposed microtubules running parallel to each other in the axon hillock and initial segment.


dynamic microtubule bundle

A microtubule bundle that undergoes changes in length, and in which microtubule sliding takes place.


static microtubule bundle

A microtubule bundle that has a constant length, and in which microtubule sliding does not take place.


Dsl1/NZR complex

A multisubunit tethering complex, i.e. a protein complex involved in mediating the initial interaction between vesicles and the membranes with which they fuse, that is involved in trafficking from the Golgi apparatus to the ER. In Saccharomyces cerevisiae the Dsl1p complex contains Dsl1p, Tip20p, and Sec39p.


Nbp35-Cfd1 ATPase complex

An iron-sulfur cluster assembly complex that is capable of weak ATPase activity. In yeast it consists of two subunits, Nbp35 and Cfd1.


iron-sulfur cluster assembly complex

A protein complex capable of assembling an iron-sulfur (Fe-S) cluster.


peri-centrosomal recycling endosome

A recycling endosome that is organized around the microtubule organizing center, close to the nucleus. This is the main recycling endosome of most cells. It receives input from the Golgi as well as recycled molecules from early endosomes.


A protein complex that consists of fibronectin bound to tissue transglutaminase, and is involved in cell adhesion.


intracellular ferritin complex

A ferritin complex located in the cell. Intracellular ferritin complexes contain 24 subunits, in a mixture of L (light) chains and H (heavy) chains.


amino acid transport complex

A heteromeric protein complex consisting of a multi-transmembrane spanning subunit (the light chain) and a type II glycoprotein subunit (the heavy chain) that functions to transport amino acids across a plasma membrane.


repressor ecdysone receptor complex

A protein complex consisting of a heterodimer of Ecdysone receptor (EcR) and ultraspiracle (usp) plus an associated corepressor such as SMRTER, which represses transcription of target genes.


cellular bud tip polarisome

Protein complex that has a role in determining cell polarity, found at the tip of a growing fungal bud.


radial spoke head 1

The portion of the radial spoke 1 that is orthogonal to the elongated stalk and which projects towards the central pair of microtubules within the ciliary axoneme.


radial spoke head

Protein complex forming portion of the radial spoke that is orthogonal to the elongated stalk and which projects towards the central pair of microtubules within the ciliary or flagellum axoneme.


radial spoke head 2

The portion of the radial spoke 2 that is orthogonal to the elongated stalk and which projects towards the central pair of microtubules within the ciliary axoneme.


radial spoke head 3

The portion of the radial spoke 3 that is orthogonal to the elongated stalk and which projects towards the central pair of microtubules within the ciliary axoneme.


mineralized avascular GAG-rich matrix

biolink:GrossAnatomicalStructure biolink:AnatomicalEntity biolink:OrganismalEntity biolink:BiologicalEntity biolink:NamedThing biolink:PhysicalEssence biolink:SubjectOfInvestigation biolink:ThingWithTaxon biolink:PhysicalEssenceOrOccurrent

Avascular GAG-rich matrix that is mineralized.


avascular GAG-rich matrix

Proteinaceous extracellular matrix that is avascular and consists primarily of glycosaminoglycans.


non-mineralized avascular GAG-rich matrix

Avascular GAG-rich matrix that is not mineralized.


An enzyme complex composed of two catalytic alpha subunits, which form a catalytic dimer, and a non-catalytic, regulatory beta subunit; the catalytic dimer may be an alpha1/alpha1 or alpha2/alpha2 homodimer, or an alpha1/alpha2 heterodimer. Modulates the action of platelet-activating factor (PAF).


icosahedral viral capsid, collar fiber

A fiber attached to the collar structure of some icosahedral viral capsids.


BLOC-3 complex

A protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. The human complex contains the Hps1 and Hps4 proteins.


BLOC complex

Any of several protein complexes required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes, platelet dense granules, and other related organelles; acronym for biogenesis of lysosomal-related organelles complex.


BLOC-1 complex

A protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. Many of the protein subunits are conserved between mouse and human; the mouse complex contains the Pallidin, Muted, Cappuccino, Dysbindin, Snapin, BLOS1, BLOS2, AND BLOS3 proteins.


BLOC-2 complex

A protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. The human complex contains the Hps3, Hps5, and Hps6 proteins; the mouse complex contains ru2 and ru.


serine-tRNA ligase complex

A heterodimeric enzyme complex that catalyzes the ligation of serine to tRNA(Ser), forming L-seryl-tRNA(Ser).


Ycf2/FtsHi complex

A protein complex located in the chloroplast inner membrane and facing the stroma that is associated with the chloroplast inner membrane translocase complex and provides the ATPase motor activity to drive import of proteins into the chloroplast stroma.


lumenal side of smooth endoplasmic reticulum membrane

The side (leaflet) of the smooth endoplasmic reticulum membrane that faces the lumen.


lumenal side of endoplasmic reticulum membrane

The side (leaflet) of the plasma membrane that faces the lumen.


lumenal side of rough endoplasmic reticulum membrane

The side (leaflet) of the rough endoplasmic reticulum membrane that faces the lumen.


plasma membrane proton-transporting ATP synthase, stator stalk

One of two stalks that connect the catalytic core of the hydrogen-transporting ATP synthase to the plasma membrane-associated F0 proteins; is thought to prevent futile rotation of the catalytic core. Examples of this component are found in Bacterial species.


proton-transporting ATP synthase, stator stalk

One of two stalks that connect the catalytic core of the hydrogen-transporting ATP synthase to the membrane-associated Fo proteins; is thought to prevent futile rotation of the catalytic core.


mitochondrial proton-transporting ATP synthase, stator stalk

One of two stalks that connect the catalytic core of the hydrogen-transporting ATP synthase to the mitochondrial membrane-associated F0 proteins; is thought to prevent futile rotation of the catalytic core.


rhabdomere membrane

The portion of the plasma membrane surrounding the rhabdomere.


Tle3-Aes complex

A transcriptional repressor complex that consists of a heterodimer of the proteins Tle3 (also known as Grg3b) and Aes (Grg5), which are homologs of the Drosophila groucho gene product.


RNA polymerase II transcription repressor complex

A protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase II promoter.


Cyc8(Ssn6)-Tup1 general repressor complex

A corepressor complex containing the WD-repeat protein Tup1p (S. cerevisiae) and Tup11/Tup12 (fission yeast) and the TPR repeat protein Cyc8p (S. cerevisiae) ssn6 (fission yeast) that is recruited to target genes by DNA-bound repressor proteins preferentially at regions where histones are deacetylated by the Clr6 class I HDAC, and recruits the SWI/SNF and SAGA complexes to promoters.


negative cofactor 2 complex

A heterodimeric protein complex that can stably associate with TATA-binding protein on promoters, thereby preventing the assembly of transcription factors TFIIA and TFIIB and leading to repression of RNA polymerase II transcription. The two subunits, NC2alpha (Drap1) and NC2beta (Dr1), dimerize through histone fold domains of the H2A/H2B type present in the amino termini.


DRM complex

A transcriptional repressor complex that contains the lin-9, lin-35, lin-37, lin-52, lin-53, lin-5is involved in 4-, dpl-1 and efl-1 proteins, and is involved in cell fate specification.


beta-catenin-ICAT complex

Transcription factor complex that inhibits binding of Tcf to beta-catenin while preserving interaction of catenin with cadherin thus inhibiting transcription mediated by beta-catenin-Tcf complex.


Mad-Max-mSin3A complex

A transcriptional repressor complex that contains a heterodimer of the bHLH-ZIP proteins Mad and Max, plus mSin3A, a homolog of the yeast Sin3p.


Mad-Max complex

A transcriptional repressor complex that consists of a heterodimer of the bHLH-ZIP proteins Mad and Max.


collagen and cuticulin-based cuticle extracellular matrix

A collagen and cuticulin-based noncellular, multilayered structure that is synthesized by an underlying ectodermal (hypodermal) cell layer. The cuticle serves essential functions in body morphology, locomotion, and environmental protection. An example of this component is found in Caenorhabditis elegans.


chitin-based extracellular matrix

Any constituent part of a chitin-based noncellular, hardened, or membranous extracellular matrix secreted from the apical surface of an epithelial sheet.


perineuronal net

A dense extracellular matrix (ECM) that forms around many neuronal cell bodies and dendrites late in development and is responsible for synaptic stabilization in the adult brain.


An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells.


fertilization envelope

A structure that lies outside the plasma membrane and surrounds the egg. The fertilization envelope forms from the vitelline membrane after fertilization as a result of cortical granule release.


basement membrane

A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.


hyaline layer

A multilayered extraembryonic matrix that functions as a substrate for cell adhesion through early development. It is thought to protect and lubricate the embryo, stabilize the blastomeres during morphogenesis, and regulate nutrient intake. The major constituent of the hyaline layer is the protein hyalin. This matrix has been found in echinoderms.


fungal biofilm matrix

An extracellular matrix lying external to fungal cells. The fungal biofilm matrix consists of polysaccharides, proteins, lipids, and nucleic acids. Fungal biofilms mediate adherence to host tissues, and provide protection from host immune defenses.


biofilm matrix

A structure lying external to microbial cells. A biofilm is an aggregate of surface-associated cells, and the biofilm matrix is the envelope of polymeric substances that surrounds the cells.


egg coat

A specialized extracellular matrix that surrounds the plasma membrane of the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development.


bacterial biofilm matrix

A structure lying external to bacterial cells. A biofilm is an aggregate of surface-associated bacteria, and the biofilm matrix is the envelope of polymeric substances that surrounds the bacteria.


organomineral extracellular matrix

An extracellular matrix consisting of a densely packed organomineral assembly in which the mineral phase represents the majority of the material by weight.


perisynaptic extracellular matrix

The portion of the extracellular matrix that lies within the perisynaptic space.


synapse-associated extracellular matrix

The extracellular matrix of the perisynaptic space (the extracellular space adjacent to the synapse) and the synaptic cleft.


interstitial matrix

A type of extracellular matrix found in interstitial connective tissue, characterized by the presence of fibronectins, proteoglycans, and types I, III, V, VI, VII and XII collagens.


interphotoreceptor matrix

A specialized extracellularc matrix that surrounds the photoreceptors of the retina and lies between them and the apical surface of the retinal pigment epithelium. The IPM has been implicated in several important activities required for photoreceptor function and maintenance.


pollen coat

A layer of extracellular matrix deposited onto the surface of the pollen wall upon disintegration of the tapetal layer of the anther wall in the late stages of pollen development. The composition of this material is highly heterogeneous and includes waxes, lipid droplets, small aromatic molecules, and proteins. The pollen coat is proposed to have many functions, such as holding pollen in the anther until dispersal, facilitation of pollen dispersal, protection of pollen from water loss and UV radiation, and facilitation of adhesion of pollen to the stigma.


mineralized extracellular matrix

Extracellular matrix that is mineralized.


vitelline envelope

A glycoprotein-based structure that lies outside the plasma membrane and surrounds the egg before fertilization.


adhesive extracellular matrix

A extracellular matrix which attaches an organism to a substrate.


ATG2-ATG18 complex

A protein complex essential for autophagy during nutrient deprivation, a catabolic process that sequesters undesired cellular material into autophagosomes for delivery to lysosomes for degradation. Contributes to nutrition homeostasis and damage control in eukaryotic cells. Functions at a late step of autophagosome formation for efficient completion of sequestration, probably through facilitating recruitment of ATG8-phosphatidylethanolamine (PE) to the preautophagosomal structure (PAS) and/or its protection from deconjugation by ATG4. Composed of ATG2 and ATG18 in Saccharomyces cerevisiae.


elongin complex

A transcription elongation factor complex that suppresses RNA polymerase II pausing, and may act by promoting proper alignment of the 3'-end of nascent transcripts with the polymerase catalytic site. Consists of a transcriptionally active Elongin A subunit (about 100 kDa) and two smaller Elongin B (about 18 kDa) and Elongin C (about 15 kDa) subunits.


Schwann cell microvillus

Small finger-like extension of a Schwann cell that contacts the nodal membrane.


inner dense plaque of desmosome

The desmosomal part containing the C-termini of desmoplakins which interact with the keratin intermediate filaments, serving to tether the intermediate filaments to the plasma membrane.


mitochondrion-derived vesicle

A vesicle derived via budding from a mitochondrion. These vesicles often contain inner membrane and, much more rarely, cristae.


intracellular vesicle

Any vesicle that is part of the intracellular region.


post-lysosomal vacuole

A membrane-bounded intracellular vesicle formed late in the endocytic pathway when the pH in the vacuole becomes neutral prior to exocytosis.


platelet alpha granule

A secretory organelle found in blood platelets, which is unique in that it exhibits further compartmentalization and acquires its protein content via two distinct mechanisms: (1) biosynthesis predominantly at the megakaryocyte (MK) level (with some vestigial platelet synthesis) (e.g. platelet factor 4) and (2) endocytosis and pinocytosis at both the MK and circulating platelet levels (e.g. fibrinogen (Fg) and IgG).


piccolo-bassoon transport vesicle

A cytoplasmic dense-core vesicle that transports a range of proteins including piccolo, bassoon, N-cadherin and syntaxin. The transported proteins may be associated with the external side of the vesicle, rather than being contained within the vesicle, therefore forming an aggregate of vesicle and proteins. Piccolo-bassoon transport vesicles (or PTVs) range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. They are packaged via the trans-Golgi network before being transported through the axon.


merozoite dense granule

Electron-dense organelle with a granular internal matrix found throughout the merozoite life cycle stage of apicomplexan parasites; contains proteins destined to be secreted into the parasitophorous vacuole following parasite invasion of a host cell.


zymogen granule

A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme.


clathrin-coated vesicle

A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.


chloroplast vesicle

A intracellular vesicle that is part of a chloroplast.


virion transport vesicle

A vesicle used to transport the partial or complete virion between cellular compartments.


bacteroid-containing symbiosome

A symbiosome containing any of various structurally modified bacteria, such as those occurring on the root nodules of leguminous plants.


epidermal lamellar body

A specialized secretory organelle found in keratinocytes and involved in the formation of an impermeable, lipid-containing membrane that serves as a water barrier and is required for correct skin barrier function.


food vacuole

Vacuole within a parasite used for digestion of the host cell cytoplasm. An example of this component is found in the Apicomplexa.


synaptic vesicle, readily releasable pool

A synaptic vesicle belonging to the pool of vesicles that are the first to be released as a result of chemical or electrical stimulation e.g. by an action potential, have the highest presynaptic membrane fusion probability and correspond to about 1% of the total number of synaptic vesicles at a resting terminal bouton.


insulin-responsive compartment

A small membrane-bounded vesicle that releases its contents by exocytosis in response to insulin stimulation; the contents are enriched in GLUT4, IRAP and VAMP2.


A cytoplasmic vesicle composed of both tubulovesicular and clear core vesicles that transport synaptic vesicle-associated proteins. Proteins carried by synaptic vesicle protein transport vesicles (STVs) include synaptophysin, synapsin Ia, synaptotagmin and synaptobrevin/vesicle-associated membrane protein 2 (VAMP2). STVs are packaged via the trans-Golgi network before being transported through the axon.


chitosome

An intracellular membrane-bounded particle found in fungi and containing chitin synthase; it synthesizes chitin microfibrils. Chitin synthase activity exists in chitosomes and they are proposed to act as a reservoir for regulated transport of chitin synthase enzymes to the division septum.


COPI-coated inter-Golgi transport vesicle

A vesicle that mediates transport of cargo within the Golgi complex (for example, between cisternae of the Golgi stack).


early endosome

A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.


melanosome

A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.


neuronal dense core vesicle

A dense core vesicle (granule) that is part of a neuron. These vesicles typically contain neuropeptides. They can be found in all parts of neurons, including the soma, dendrites, axonal swellings (varicosities) and synaptic terminals.


clathrin-sculpted gamma-aminobutyric acid transport vesicle

A clathrin-sculpted lipid bilayer membrane-enclosed vesicle after clathrin release and containing gamma-aminobutyric acid transport vesicle.


leucosome

A tissue-specific, membrane-bounded cytoplasmic organelle within which uric acid and/or purines crystalize in reflective stacks. Leucosomes are synthesized in leucophore cells and have a whitish cast.


pigment granule

A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes.


clathrin-coated endocytic vesicle

A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance.


carotenoid vesicle

A tissue-specific cytoplasmic vesicle surrounded by a membrane half-leaflet within which carotenoid pigments are stored. Carotenoid vesicles are synthesized in xanthophores and erythrophore cells and are yellow, orange or red in appearance.


early phagosome

A membrane-bounded intracellular vesicle as initially formed upon the ingestion of particulate material by phagocytosis.


pexophagosome

A membrane-bounded intracellular vesicle involved in the degradation of peroxisome by macropexophagy.


mucocyst

A small subcellular vesicle, surrounded by a membrane, in the pellicle of ciliate protozoans that discharges a mucus-like secretion.


dense core granule

Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted.


cortical granule

A secretory vesicle that is stored under the cell membrane of an egg. These vesicles fuse with the egg plasma membrane as part of egg activation and are part of the block to polyspermy.


sorting endosome

A multivesicular body surrounded by and connected with multiple tubular compartments with associated vesicles.


gut granule

A lysosome-related organelle contained within the intestinal cells of the nematode C. elegans. Gut granules are acidified, birefringent, autofluorescent, and contain the vacuolar H+-ATPase. They also serve as sites of cellular zinc storage.


pinosome

A membrane-bounded, uncoated intracellular vesicle formed by the process of pinocytosis.


multivesicular body, internal vesicle

A membrane-bounded vesicle wholly contained within a multivesicular body.


clathrin-sculpted vesicle

A clathrin-sculpted lipid bilayer membrane-enclosed vesicle after clathrin release.


COPI-coated vesicle

A vesicle with a coat formed of the COPI coat complex proteins. COPI-coated vesicles are found associated with Golgi membranes at steady state, are involved in Golgi to endoplasmic reticulum (retrograde) vesicle transport, and possibly also in intra-Golgi transport.


synaptic vesicle, recycling pool

A synaptic vesicle belonging to the pool that repopulate vacancies within the readily releasable pool (RRP) of synaptic vesicles, and require more significant stimuli than the RRP in order to release neurotransmitter; about 10-15% of the total number of synaptic vesicles at a resting terminal bouton are in this state.


alveolar lamellar body

A specialized secretory organelle found in type II pneumocytes and involved in the synthesis, secretion, and reutilization of pulmonary surfactant.


neurosecretory vesicle

A large cytoplasmic membrane-bounded vesicle with an electron dense granular core, up to 150-200 nm in diameter, found in neurosecretory cells in the hypothalamus.


clathrin-coated phagocytic vesicle

A clathrin-coated, membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.


postsynaptic recycling endosome

A recycling endosome of the postsynapse. In postsynaptic terminals with dendritic spines, it is typically located at the base of a dendritic spine. It is involved in recycling of neurotransmitter receptors to the postsynaptic membrane. In some cases at least, this recycling is activated by postsynaptic signaling and so can play a role in long term potentiation.


coated vesicle

Small membrane-bounded organelle formed by pinching off of a coated region of membrane. Some coats are made of clathrin, whereas others are made from other proteins.


ciliary vesicle

A Golgi-derived vesicle to which the ciliary basal body docks via its transitional fibers. Its membrane is compositionally distinct from Golgi membranes, and will become the ciliary membrane once the ciliary vesicle is fused to the plasma membrane. The ciliary vesicle is thought to be formed by multiple smaller vesicles that attach to the transitional fibers and then fuse to form a larger vesicle.


platelet dense granule

Electron-dense granule occurring in blood platelets that stores and secretes adenosine nucleotides and serotonin. They contain a highly condensed core consisting of serotonin, histamine, calcium, magnesium, ATP, ADP, pyrophosphate and membrane lysosomal proteins.


micropinosome

A membrane-bounded, uncoated intracellular vesicle formed by the process of micropinocytosis.


transport vesicle

Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.


synaptic vesicle

A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.


endosome to plasma membrane transport vesicle

A transport vesicle that mediates transport from the endosome to the plasma membrane, and fuses with the plasma membrane to deliver lipids and membrane proteins to the plasma membrane and to release various cargo molecules, such as proteins or hormones, by exocytosis.


Golgi to plasma membrane transport vesicle

A transport vesicle that mediates transport from the Golgi to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.


dendritic lamellar body

A specialized secretory organelle found in neurons and associated with the formation of dendrodendritic gap junctions.


recycling endosome

An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.


azurophil granule

Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.


symbiosome

A double-enveloped cell compartment, composed of an endosymbiont with its plasmalemma (as inner envelope) and a non-endosymbiotic outer envelope (the perisymbiontic membrane).


lamellar body

A membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome.


contractile vacuole

A specialized vacuole of eukaryotic cells, especially Protozoa, that fills with water from the cytoplasm and then discharges this externally by the opening of contractile vacuole pores. One of its functions is osmoregulatory.


aleurone grain

A membrane-bounded storage granule found in cells of the aleurone layer in plants; contains either a protein matrix, protein-carbohydrate bodies and/or globoids. Aleurone grains are formed by the vacuole, rough endoplasmic reticulum and dictyosomes.


clathrin-sculpted acetylcholine transport vesicle

A clathrin-sculpted lipid bilayer membrane-enclosed vesicle after clathrin release and containing acetylcholine.


Cvt vesicle

A cytosolic vesicle that is enclosed by a double membrane and is implicated in the cytoplasm to vacuole targeting pathway. These vesicles are found in the yeast S. cerevisiae, and contain vacuolar hydrolases, aminopeptidase I (Ape1p) and alpha-mannosidase (Ams1p).


acrosomal vesicle

A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.


COPII-coated ER to Golgi transport vesicle

A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).


secretory vesicle

A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.


apical recycling endosome

Tubulo-vesicular structure located in the apical cytoplasm that participates in apical cargo recycling in polarized epithelial cells.


organellar chromatophore

A bacteroid-containing symbiosome in which the bacterial component is a genetically highly reduced cyanobacterium that is photosynthetically active and incapable of an independent existence outside its host. The chromatophore functions as a photosynthetic organelle, and has been found and characterized in the amoeba Paulinella chromatophora.


phagolysosome

A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes.


cyanosome

A tissue-specific, membrane-bounded cytoplasmic organelle within which an unknown blue pigment is localized. Cyanosomes are synthesized in cyanophores and are blue in appearance.


Golgi-associated vesicle

Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.


amorphous vesicle

A cytoplasmic membrane-bounded vesicle first described in dendrites, categorized by smooth membranes, electron-lucent interiors and irregular shapes. Sometimes occurs in clumps. Amorphous vesicles have been found to contain material taken up from the extracellular space, therefore suggesting that they may be part of the endosomal pathway.


specific granule

Granule with a membranous, tubular internal structure, found primarily in mature neutrophil cells. Most are released into the extracellular fluid. Specific granules contain lactoferrin, lysozyme, vitamin B12 binding protein and elastase.


osmiophilic body

A membrane-bounded vesicle found predominantly in Plasmodium female gametocytes, that becomes progressively more abundant as the gametocyte reaches full maturity. These vesicles lie beneath the subpellicular membrane of the gametocyte, and the release of their contents into the parasitophorous vacuole has been postulated to aid in the escape of gametocytes from the erythrocyte after ingestion by the mosquito.


clathrin-sculpted monoamine transport vesicle

A clathrin-sculpted lipid bilayer membrane-enclosed vesicle after clathrin release and containing monoamines.


pterinosome

A tissue-specific, membrane-bounded cytoplasmic organelle within which pteridine pigments are synthesized and stored. Pterinosomes are synthesized in xanthophores and erythrophore cells and are yellow, orange or red in appearance.


chromaffin granule

Specialized secretory vesicle found in the cells of adrenal glands and various other organs, which is concerned with the synthesis, storage, metabolism, and secretion of epinephrine and norepinephrine.


sperm cytoplasmic droplet

A small amount of cytoplasm surrounded by a cell membrane that is generally retained in spermatozoa after spermiogenesis, when the majority of the cytoplasm is phagocytosed by Sertoli cells to produce what are called residual bodies. Initially, the droplet is located at the neck just behind the head of an elongated spermatid. During epididymal transit, the cytoplasmic droplet migrates caudally to the annulus at the end of the midpiece; the exact position and time varies by species. The cytoplasmic droplet consists of lipids, lipoproteins, RNAs, a variety of hydrolytic enzymes, receptors, ion channels, and Golgi-derived vesicles. The droplet may be involved in regulatory volume loss (RVD) at ejaculation, and in most species, though not in humans, the cytoplasmic droplet is lost at ejaculation. Note that the cytoplasmic droplet is distinct from 'excessive residual cytoplasm' that sometimes remains in epididymal spermatozoa, particularly when spermiogenesis has been disrupted.


presynaptic endosome

An endosome present in the presynapse that fuses with endocytic vesicles arising in the presynaptic endocytic zone. This organelle is believed to be involved in regeneration of synaptic vesicles.


fusiform vesicle

A cytoplasmic vesicle which contains two urothelial plaques and can deliver these plaques to the apical plasma membrane of urothelial superficial (umbrella) cells. It can also be formed by endocytosis of apical plasma membrane during contractions of the urinary bladder.


macropinosome

A membrane-bounded, uncoated intracellular vesicle formed by the process of macropinocytosis.


granular vesicle

A cytoplasmic membrane-bounded vesicle of varying size, but usually larger than 45 nm, with an electron dense granular core, found in noradrenergic and peptidergic cells.


ficolin-1-rich granule

Highly exocytosable gelatinase-poor granules found in neutrophils and rich in ficolin-1. Ficolin-1 is released from neutrophil granules by stimulation with fMLP or PMA, and the majority becomes associated with the surface membrane of the cells and can be detected by flow cytometry.


esterosome

A vesicle filled with crystalline protein that shows sequence similarities with various esterases.


endosome

A vacuole to which materials ingested by endocytosis are delivered.


basolateral recycling endosome

Tubulo-vesicular structure located in the basolateral cytoplasm that participates in basolateral cargo recycling in polarized epithelial cells.


endolysosome

An transient hybrid organelle formed by fusion of a late endosome with a lysosome, and in which active degradation takes place.


pericanalicular vesicle

A membrane-bounded vesicle found near the apical, or pericanalicular, membrane of a hepatocyte; contains proteins involved in bile salt transport and other fluid and solute transport processes.


postsynaptic early endosome

An early endosome of the postsynapse. It acts as the major sorting station on the endocytic pathway, targeting neurotransmitter receptors for degregation or recycling.


tertiary granule

A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells.


postsynaptic endosome

An endosomal compartment that is part of the post-synapse. Only early and recycling endosomes are typically present in the postsynapse.


CGRP receptor complex

A transmembrane, G protein-coupled signaling receptor complex recognized by calcitonin gene-related peptides (CGRP).


calcitonin family receptor complex

A protein complex which is capable of calcitonin family receptor activity. Calcitonin family receptors may form dimers, trimers or tetramers; adrenomedullin and amylin receptors have only been observed as dimers so far.


adrenomedullin receptor complex

A transmembrane, G protein-coupled signaling receptor complex which is capable of adrenomedullin receptor activity.


amylin receptor complex 3

A G protein-coupled receptor complex that serves as a receptor for amylin polypeptide (AMY) and consists of a calcitonin receptor (CTR/CALCR) and a receptor activity-modifying protein (RAMP) 3. Amylin receptor complex 3 (AMY3) also serves as a receptor for the amyloid-beta complex. Ligand binding to AMY3 results in increased cytosolic calcium ion levels and in activation on multiple intracellular signaling pathways.


amylin receptor complex

A protein complex which is capable of amylin receptor activity.


amylin receptor complex 1

A G protein-coupled receptor complex that serves as a receptor for amylin polypeptide (AMY) and consists of a calcitonin receptor (CTR/CALCR) and a receptor activity-modifying protein (RAMP) 1. Amylin receptor complex 1 (AMY1) also serves as a receptor for the calcitonin related peptide (CGRP) and adrenomedullin (AM/ADM).


amylin receptor complex 2

A G protein-coupled receptor complex that serves as a receptor for amylin polypeptide (AMY) and consists of a calcitonin receptor (CTR/CALCR) and a receptor activity-modifying protein (RAMP) 2. Amylin receptor complex 2 (AMY2) also serves as a receptor for adrenomedullin (AM/ADM).


MutS complex

A homodimeric mismatch repair complex involved in binding to and correcting insertion/deletion mutations.


mismatch repair complex

Any complex formed of proteins that act in mismatch repair.


MutSalpha complex

A heterodimer involved in the recognition and repair of base-base and small insertion/deletion mismatches. In human the complex consists of two subunits, MSH2 and MSH6.


MutSgamma complex

A heterodimer involved in the stabilization of DNA recombination intermediates, the promotion of crossover recombination, and the proper assembly of the synaptonemal complex in meiotic prophase nuclei. In yeast the complex consists of two subunits, Msh4 and Msh5.


MutLbeta complex

A heterodimer involved in the recognition of base-base and small insertion/deletion mismatches. In human the complex consists of two subunits, MLH1 and PMS1.


MutSbeta complex

A heterodimer involved in binding to and correcting insertion/deletion mutations. In human the complex consists of two subunits, MSH2 and MSH3.


MutLalpha complex

A heterodimer involved in the recognition of base-base and small insertion/deletion mismatches. In human the complex consists of two subunits, MLH1 and PMS2.


MutLgamma complex

A heterodimer involved in the recognition of base-base and small insertion/deletion mismatches. In S. cerevisiae the complex consists of two subunits, Mlh1 and Mlh3.


MAML2-RBP-Jkappa-ICN4 complex

A protein complex that consists of the intracellular domain of Notch4 (ICN4), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-2 (MAML2); the complex is involved in transcriptional activation in response to Notch-mediated signaling.


A protein complex that contains the cell adhesion molecules protocadherin-alpha-v4 and protocadherin-gamma-b2, and is involved in the regulation of protein localization to the plasma membrane.


Hrd1p ubiquitin ligase ERAD-L complex

A multiprotein complex that recognizes and ubiquitinates proteins with misfolded luminal domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Hrd1p.


brahma complex

A SWI/SNF-type complex that contains 8 to 14 proteins, including both conserved (core) and nonconserved components; contains the ATPase product of the Drosophila brm (brahma) or mammalian SMARCA2/BAF190B/BRM gene, or an ortholog thereof.


TIM23 mitochondrial import inner membrane translocase complex

The protein transport machinery of the mitochondrial inner membrane that typically transports proteins that possess a matrix-targeting N-terminal presequence. The TIM23 complex contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor.


tubovesicular membrane network

A complex, symbiont-induced host-derived organelle that is comprised of multiple protein and lipid domains.


Grb2-EGFR complex

A protein complex that contains the epidermal growth factor receptor (EGFR) and Grb2, and is involved in linking EGFR activation to the p21-Ras pathway.


mitochondrial endopeptidase Clp complex

A Clp endopeptidase complex located in the mitochondrion.


SWI/SNF complex

A SWI/SNF-type complex that contains 8 to 14 proteins, including both conserved (core) and nonconserved components; contains the ATPase product of the yeast SNF2 or mammalian SMARCA4/BAF190A/BRG1 gene, or an ortholog thereof.


signal recognition particle, plasma membrane targeting

A complex consisting of a protein and RNA component which binds the signal sequence of some proteins and facilitates their export to or across the plasma membrane.


centriolar satellite

A small (70-100 nm) cytoplasmic granule that contains a number of centrosomal proteins; centriolar satellites traffic toward microtubule minus ends and are enriched near the centrosome.


transcription factor TFIIIB-alpha complex

A transcription factor TFIIIB-beta complex that contains the TATA-binding protein (TBP), B'' and a specialized homolog of the conserved subunit BRF referred to as BRFU or TFIIIB50, which found in human but not conserved in yeast; the complex is involved in the regulation of transcription from type 3 (upstream) RNA polymerase III promoters.


sperm connecting piece

The segment of the sperm flagellum that attaches to the implantation fossa of the nucleus in the sperm head; from the remnant of the centriole at this point, the axoneme extends throughout the length of the flagellum.


Golgi trans cisterna membrane

The lipid bilayer surrounding any of the thin, flattened compartments that form the trans portion of the Golgi complex.


Golgi cisterna membrane

The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.


Golgi medial cisterna membrane

The lipid bilayer surrounding any of the thin, flattened compartments that form the medial portion of the Golgi complex.


Golgi cis cisterna membrane

The lipid bilayer surrounding any of the thin, flattened compartments that form the cis portion of the Golgi complex.


myosin V complex

A myosin complex containing a dimer of class V myosin heavy chains and associated light chains; involved in intracellular transport. Myosin V is a dimeric molecule consisting of conserved motor domains followed by 6 IQ motifs which bind specific light chains and calmodulin. The tail domain is important for cellular localization and cargo binding and can be divided into an alpha-helical coiled coil region and a C-terminal globular region.