LiteFold/GO huggingface dataset:
cytoplasmic dynein complex (GO:0005868)
Namespace: cellular_component
Definition: Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains.
Synonyms: cytoplasmic dynein heavy chain; cytoplasmic dynein intermediate chain; cytoplasmic dynein intermediate light chain; cytoplasmic dynein light chain
Comment: Note that this term is labelled based on phylogenetic classification and community usage, rather than strict cellular localization. Cytoplasmic dynein complexes may contain ciliary dyneins; therefore the term is not linked to 'cytoplasm'. Cytoplasmic dynein complexes do not contain axonemal dyneins; see GO:0005858 axonemal dynein complex.
dynactin complex (GO:0005869)
Namespace: cellular_component
Definition: A 20S multiprotein assembly of total mass about 1.2 MDa that activates dynein-based activity in vivo. A large structural component of the complex is an actin-like 40 nm filament composed of actin-related protein, to which other components attach.
actin capping protein of dynactin complex (GO:0005870)
Namespace: cellular_component
Definition: A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, nucleates the polymerization of actin monomers but does not sever actin filaments, and which is a part of the dynactin complex.
kinesin complex (GO:0005871)
Namespace: cellular_component
Definition: Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
minus-end kinesin complex (GO:0005872)
Namespace: cellular_component
Definition: Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the minus end of a microtubule.
plus-end kinesin complex (GO:0005873)
Namespace: cellular_component
Definition: Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the plus end of a microtubule.
microtubule (GO:0005874)
Namespace: cellular_component
Definition: Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
Synonyms: microtubuli; microtubulus; neurotubule
microtubule associated complex (GO:0005875)
Namespace: cellular_component
Definition: Any multimeric complex connected to a microtubule.
nuclear microtubule (GO:0005880)
Namespace: cellular_component
Definition: Any microtubule in the nucleus of a cell.
cytoplasmic microtubule (GO:0005881)
Namespace: cellular_component
Definition: Any microtubule in the cytoplasm of a cell.
Synonyms: non-spindle-associated astral microtubule
intermediate filament (GO:0005882)
Namespace: cellular_component
Definition: A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.
Synonyms: intermediate filament associated protein; type I intermediate filament associated protein; type II intermediate filament associated protein
actin filament (GO:0005884)
Namespace: cellular_component
Definition: A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
Synonyms: microfilament
Arp2/3 protein complex (GO:0005885)
Namespace: cellular_component
Definition: A stable protein complex that contains two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5), and functions in the nucleation of branched actin filaments.
plasma membrane (GO:0005886)
Namespace: cellular_component
Definition: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
Synonyms: bacterial inner membrane; cell membrane; cellular membrane; cytoplasmic membrane; inner endospore membrane; integral component of plasma membrane; integral to plasma membrane; juxtamembrane; plasma membrane lipid bilayer; plasmalemma
obsolete proteoglycan integral to plasma membrane (GO:0005888)
Namespace: cellular_component
Definition: OBSOLETE. Penetrating at least one phospholipid bilayer of a plasma membrane and consisting of proteoglycan. Also refers to the state of being buried in the bilayer with no exposure outside the bilayer.
Synonyms: proteoglycan integral to plasma membrane
Comment: This term was made obsolete because it describes the composition (i.e. proteoglycan) and not the location of a gene product.
sodium:potassium-exchanging ATPase complex (GO:0005890)
Namespace: cellular_component
Definition: Sodium:potassium-exchanging ATPases are tetrameric proteins, consisting of two large alpha subunits and two smaller beta subunits. The alpha subunits bear the active site and penetrate the membrane, while the beta subunits carry oligosaccharide groups and face the cell exterior.
Synonyms: sodium pump; sodium/potassium-exchanging ATPase complex
voltage-gated calcium channel complex (GO:0005891)
Namespace: cellular_component
Definition: A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.
Synonyms: voltage gated calcium channel complex; voltage-dependent calcium channel complex; voltage-sensitive calcium channel complex
acetylcholine-gated channel complex (GO:0005892)
Namespace: cellular_component
Definition: A homo- or hetero-pentameric protein complex that forms a transmembrane channel through which ions may pass in response to acetylcholine binding.
Synonyms: nicotinic acetylcholine receptor; nicotinic acetylcholine-gated receptor-channel complex
interleukin-2 receptor complex (GO:0005893)
Namespace: cellular_component
Definition: A protein complex that binds interleukin-2; comprises alpha, beta, and gamma subunits.
Synonyms: IL-2 receptor complex
interleukin-3 receptor complex (GO:0005894)
Namespace: cellular_component
Definition: A protein complex that binds interleukin-3; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-3 receptor, whereas the beta chain is shared with the receptors for granulocyte-macrophage colony-stimulating factor and interleukin-5.
Synonyms: IL-3 receptor complex
interleukin-5 receptor complex (GO:0005895)
Namespace: cellular_component
Definition: A protein complex that binds interleukin-3; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-5 receptor, whereas the beta chain is shared with the receptors for granulocyte-macrophage colony-stimulating factor and interleukin-3.
Synonyms: IL-5 receptor complex
interleukin-6 receptor complex (GO:0005896)
Namespace: cellular_component
Definition: A hexameric protein complex consisting of two molecules each of interleukin-6, interleukin-6 receptor alpha chain, and gp-130.
Synonyms: IL-6 receptor complex
interleukin-9 receptor complex (GO:0005897)
Namespace: cellular_component
Definition: A protein complex that binds interleukin-9; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-9 receptor, whereas the beta chain is shared with the receptors for several other interleukins.
Synonyms: IL-9 receptor complex
interleukin-13 receptor complex (GO:0005898)
Namespace: cellular_component
Definition: A protein complex that binds interleukin-13; consists of two chains, interleukin-13 receptor alpha1 chain and interleukin-4 receptor alpha chain.
Synonyms: IL-13 receptor complex
insulin receptor complex (GO:0005899)
Namespace: cellular_component
Definition: A disulfide-bonded, heterotetrameric receptor complex. The alpha chains are entirely extracellular, while each beta chain has one transmembrane domain. The ligand binds to the alpha subunit extracellular domain and the kinase is associated with the beta subunit intracellular domain.
type I oncostatin-M receptor complex (GO:0005900)
Namespace: cellular_component
Definition: A heterodimeric receptor for the cytokine oncostatin-M (OSM). In humans the receptor complex is made up of the gene products gp130 and OSMR-beta.
Synonyms: oncostatin-M receptor complex
caveola (GO:0005901)
Namespace: cellular_component
Definition: A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
Synonyms: caveolae; caveolar membrane
brush border (GO:0005903)
Namespace: cellular_component
Definition: The dense covering of microvilli on the apical surface of an epithelial cell in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
clathrin-coated pit (GO:0005905)
Namespace: cellular_component
Definition: A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
Synonyms: coated pit
obsolete clathrin adaptor (GO:0005906)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: adaptin; clathrin adaptor
Comment: This term was made obsolete because it was positioned incorrectly, so the replacement term has a definition different from what this term appeared to mean.
obsolete HA1 clathrin adaptor (GO:0005907)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: AP1; HA1 clathrin adaptor
Comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology was erroneous.
obsolete HA2 clathrin adaptor (GO:0005908)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: AP2; HA2 clathrin adaptor
Comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology was erroneous.
cell-cell junction (GO:0005911)
Namespace: cellular_component
Definition: A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects.
Synonyms: cell-cell contact region; cell-cell contact zone; intercellular junction
spot adherens junction (GO:0005914)
Namespace: cellular_component
Definition: A small cell-cell adherens junction assembled during the cellularization stage of insect embyrogenesis; spot adherens junctions later fuse to form the zonula adherens.
Synonyms: dense plaque; punctum adherens
zonula adherens (GO:0005915)
Namespace: cellular_component
Definition: A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells.
Synonyms: adhesion belt; belt desmosome; intermediate junction; zonula adhaerens
fascia adherens (GO:0005916)
Namespace: cellular_component
Definition: A cell-cell junction that contains the transmembrane protein N-cadherin, which interacts with identical molecules from neighbouring cells to form a tight mechanical intercellular link; forms a large portion of the intercalated disc, the structure at which myofibrils terminate in cardiomyocytes.
nephrocyte diaphragm (GO:0005917)
Namespace: cellular_component
Definition: A specialized cell-cell junction found between nephrocytes of the insect kidney, which is adapted for filtration of hemolymph. The insect nephrocyte is anatomically and functionally similar to the glomerular podocyte of vertebrates.
Synonyms: nephrocyte junction
septate junction (GO:0005918)
Namespace: cellular_component
Definition: A cell-cell junction that forms a continuous band around each cell in an epithelium; within the septate junction the membranes of adjacent cells maintain a constant distance of approximately 15 nm; found in arthropods.
Synonyms: septate desmosome
pleated septate junction (GO:0005919)
Namespace: cellular_component
Definition: A septate junction in which regular arrays of electron-dense septae span the intermembrane space.
Synonyms: pleated desmosome
gap junction (GO:0005921)
Namespace: cellular_component
Definition: A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.
Synonyms: communicating junction; electrical synapse; electrotonic synapse; gap junction macula; gap junction plaque; intercellular gap junction channel; macula communicans; zonula communicans
connexin complex (GO:0005922)
Namespace: cellular_component
Definition: An assembly of six molecules of connexin, made in the Golgi apparatus and subsequently transported to the plasma membrane, where docking of two connexons on apposed plasma membranes across the extracellular space forms a gap junction.
Synonyms: connexon; connexon complex
bicellular tight junction (GO:0005923)
Namespace: cellular_component
Definition: An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
Synonyms: zonula occludens
obsolete cell-substrate adherens junction (GO:0005924)
Namespace: cellular_component
Definition: OBSOLETE. An adherens junction which connects a cell to the extracellular matrix.
Synonyms: hemi-adherens junction
Comment: The reason for obsoletion is that, based on the most recent literature, there is no such structure in biology as 'cell-substrate adherens junction'. An 'adherens junction' is always a 'cell-cell junction' (PMIDs: 20571587, 17854762, 21422226, 28096264, 28401269, 26923917).
focal adhesion (GO:0005925)
Namespace: cellular_component
Definition: A cell-substrate junction that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. In insects focal adhesion has also been referred to as hemi-adherens junction (HAJ).
Synonyms: adhesion plaque; connecting hemi-adherens junction; focal contact; HAJ; hemi-adherens junction
muscle tendon junction (GO:0005927)
Namespace: cellular_component
Definition: A cell-substrate junction found at the terminal anchorage site of skeletal muscle cells to tendons.
Synonyms: myotendinous junction
obsolete apical hemi-adherens junction (GO:0005928)
Namespace: cellular_component
Definition: OBSOLETE. A cell-substrate adherens junction found in the apical region of a cell, such as those found in cuticle-secreting epithelia, which connect the apical membrane to the cuticle.
Synonyms: apical cell-substrate adherens junction; apical dense plaque
Comment: The reason for obsoletion is that this term has not been used for GO annotation at all since 2001 when it was created, it has no children, it is not a part of any subset/slim.
cilium (GO:0005929)
Namespace: cellular_component
Definition: A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
Synonyms: eukaryotic flagellum; flagellum; microtubule-based flagellum; primary cilium
Comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms.
axoneme (GO:0005930)
Namespace: cellular_component
Definition: The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
Synonyms: ciliary axoneme; cilium axoneme; flagellar axoneme; flagellum axoneme
Comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane.
axonemal nexin link (GO:0005931)
Namespace: cellular_component
Definition: A protein complex found in the axoneme of eukaryotic cilia and flagella. It forms interconnections between the microtubule outer doublets that surround the inner central pair of microtubules.
Synonyms: axonemal interdoublet link; nexin complex
cellular bud tip (GO:0005934)
Namespace: cellular_component
Definition: The end of a cellular bud distal to the site of attachment to the mother cell.
cellular bud neck (GO:0005935)
Namespace: cellular_component
Definition: The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
obsolete shmoo (GO:0005936)
Namespace: cellular_component
Definition: OBSOLETE. The characteristic projection formed in response to mating pheromone by cells of Saccharomyces and other fungi with similar life cycles. Named after the Al Capp cartoon character, whose shape it resembles.
Synonyms: shmoo
Comment: This term was made obsolete because it represents a type of whole cell rather than a cellular component. To update annotations, consider the external ontology term 'shmoo ; FAO:0001023'.
mating projection (GO:0005937)
Namespace: cellular_component
Definition: The projection formed by unicellular fungi in response to mating pheromone.
Synonyms: conjugation tube; shmoo
cell cortex (GO:0005938)
Namespace: cellular_component
Definition: The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
Synonyms: cell periphery; ectoplasm; peripheral cytoplasm
septin ring (GO:0005940)
Namespace: cellular_component
Definition: A tight ring-shaped structure that forms in the division plane at the site of cytokinesis; composed of members of the conserved family of filament-forming proteins called septins as well as septin-associated proteins. This type of septin structure is observed at the bud neck of budding fungal cells, at the site of cell division in animal cells, at the junction between the mother cell and a pseudohyphal projection, and also within hyphae of filamentous fungi at sites where a septum will form.
obsolete unlocalized protein complex (GO:0005941)
Namespace: cellular_component
Definition: OBSOLETE. Used as a holding place for cellular components whose precise localization is, as yet, unknown, or has not been determined by GO (the latter is the major reason for nodes to have this parent); this term should not be used for annotation of gene products.
Synonyms: unlocalized protein complex
Comment: This term was made obsolete because it was originally intended only as a temporary parent for protein complex terms for which no more specific parents had been found. This term no longer has any children: All protein complex terms are is_a 'protein complex ; GO:0043234' and nearly all have been placed under parents to yield more specific paths traversing a part_of relationship. In other words, the term has been superseded by other terms and relationships in the cellular component ontology, and is no longer needed.
phosphatidylinositol 3-kinase complex (GO:0005942)
Namespace: cellular_component
Definition: A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too.
Synonyms: 1-phosphatidylinositol 3-kinase complex; phosphoinositide 3-kinase complex; PI3-kinase p85-subunit alpha- PI3-kinase p110 complex; PI3K complex; PIK3C3-PIK3R4 complex; PIK3CA-PIK3R1 complex
Comment: For discussion of membrane association, please see https://sourceforge.net/p/geneontology/ontology-requests/11559/
phosphatidylinositol 3-kinase complex, class IA (GO:0005943)
Namespace: cellular_component
Definition: A class I phosphatidylinositol 3-kinase complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic class IA phosphoinositide 3-kinase (PI3K) subunit and an associated SH2 domain-containing regulatory subunit that is a member of a family of related proteins often called p85 proteins. Through the interaction with the SH2-containing adaptor subunits, Class IA PI3K catalytic subunits are linked to tyrosine kinase signaling pathways.
Synonyms: 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex; 1-phosphatidylinositol-4-phosphate kinase, class IA complex; class IA PI3K complex; phosphoinositide 3-kinase complex, class IA