LiteFold/GO huggingface dataset:
endoplasmic reticulum (GO:0005783)
Namespace: cellular_component
Definition: The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
Synonyms: ER
Sec61 translocon complex (GO:0005784)
Namespace: cellular_component
Definition: A translocon complex that contains a core heterotrimer of conserved alpha, beta and gamma subunits, and may contain additional proteins (translocon-associated proteins or TRAPs); in budding yeast the core proteins are Sec61p, Sbh1p, and Sss1p. The Sec61 translocon complex functions in cotranslational and posttranslational translocation events.
Synonyms: Sec61p-Sbh1p-Sss1p complex
signal recognition particle receptor complex (GO:0005785)
Namespace: cellular_component
Definition: A transmembrane heterodimeric protein located in the membrane of the rough endoplasmic reticulum. Both subunits contain GTPase domains with which signal recognition particle interacts. In the presence of GTP and SRP receptor, SRP is released from the ribosome-nascent chain complex.
Synonyms: docking protein complex; SR complex
signal recognition particle, endoplasmic reticulum targeting (GO:0005786)
Namespace: cellular_component
Definition: A ribonucleoprotein particle of 325 kDa composed of a 7S (300 nucleotide) RNA molecule and a complex of six different polypeptides. This binds both to the N-terminal signal peptide for proteins destined for the endoplasmic reticulum as they emerge from the large ribosomal subunit and also to the ribosome. This binding arrests further translation thereby preventing the proteins from being released into the cytosol. The SRP-ribosome complex then diffuses to the endoplasmic reticulum where it is bound to the signal recognition particle receptor, which allows resumption of protein synthesis and facilitates the passage of the growing polypeptide chain through the translocon. Through a process involving GTP hydrolysis, the SRP-SRP receptor complex dissociates and SRP returns to the cytosol. Of the six polypeptides of SRP the 54 kDa subunit (SRP54) is the central player. It contains an N-terminal GTPase domain and a C-terminal domain that binds directly to the signal peptide and the SRP RNA. Examples of this component are found in Mus musculus, Saccharomyces cerevisiae and Arabidopsis thaliana.
Synonyms: signal sequence receptor complex; SRP
signal peptidase complex (GO:0005787)
Namespace: cellular_component
Definition: A protein complex that is located in the endoplasmic reticulum membrane and cleaves the signal sequence from precursor proteins following their transport out of the cytoplasmic space.
endoplasmic reticulum lumen (GO:0005788)
Namespace: cellular_component
Definition: The volume enclosed by the membranes of the endoplasmic reticulum.
Synonyms: cisternal lumen; endoplasmic reticulum cisterna; ER cisterna; ER lumen
endoplasmic reticulum membrane (GO:0005789)
Namespace: cellular_component
Definition: The lipid bilayer surrounding the endoplasmic reticulum.
Synonyms: ER membrane
rough endoplasmic reticulum (GO:0005791)
Namespace: cellular_component
Definition: The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.
Synonyms: RER; rough ER
obsolete microsome (GO:0005792)
Namespace: cellular_component
Definition: OBSOLETE. Any of the small, heterogeneous, artifactual, vesicular particles, 50-150 nm in diameter, that are formed when some eukaryotic cells are homogenized and that sediment on centrifugation at 100000 g.
Synonyms: microsomal membrane; microsome
Comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)
Namespace: cellular_component
Definition: A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
Synonyms: EGTC; endoplasmic reticulum-Golgi transport container; ER-Golgi intermediate compartment; ER-Golgi transport container; ERGIC; pre-Golgi intermediate compartment; vesicular-tubular cluster; VTC
Golgi apparatus (GO:0005794)
Namespace: cellular_component
Definition: A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
Synonyms: Golgi; Golgi complex; Golgi ribbon
Comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
Golgi stack (GO:0005795)
Namespace: cellular_component
Definition: The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.
Synonyms: dictyosome; Golgi cisternae
Golgi lumen (GO:0005796)
Namespace: cellular_component
Definition: The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
Synonyms: Golgi apparatus lumen
Golgi medial cisterna (GO:0005797)
Namespace: cellular_component
Definition: The middle Golgi cisterna (or cisternae).
Synonyms: Golgi apparatus medial cisterna
obsolete COPII vesicle (GO:0005800)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: COPII vesicle
Comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
cis-Golgi network (GO:0005801)
Namespace: cellular_component
Definition: The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum.
Synonyms: cis face; cis Golgi network; forming face; Golgi cis face; Golgi cis-face
Comment: The CGN is not considered part of the Golgi stack.
trans-Golgi network (GO:0005802)
Namespace: cellular_component
Definition: The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
Synonyms: Golgi trans face; Golgi trans-face; late Golgi; maturing face; TGN; trans face; trans Golgi network
Comment: There are different opinions about whether the TGN should be considered part of the Golgi apparatus or not. We follow Alberts et al, 1994 (ISBN:0815316194), who consider it to be a part.
obsolete secretory vesicle (GO:0005803)
Namespace: cellular_component
Definition: OBSOLETE. A small subcellular vesicle, or granule, surrounded by a single-layered membrane; formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion.
Synonyms: secretory vesicle; transition vesicle
Comment: This term was made obsolete because it was being used to describe two different components.
obsolete secretory vesicle membrane (GO:0005804)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: secretory vesicle membrane
Comment: This term was made obsolete because its parent was made obsolete.
obsolete ER-Golgi transport vesicle (GO:0005805)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: ER-Golgi transport vesicle
Comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
obsolete Golgi-ER transport vesicle (GO:0005806)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: Golgi-ER transport vesicle
Comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
obsolete Golgi-plasma membrane transport vesicle (GO:0005808)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: Golgi-plasma membrane transport vesicle
Comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; a personal communication from John Armstrong indicated that a replacement term was not required, as TGN-Golgi transport is likely to be mediated by tubules rather than vesicles.
obsolete Golgi-vacuole transport vesicle (GO:0005809)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: Golgi-vacuole transport vesicle
Comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
obsolete endocytotic transport vesicle (GO:0005810)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: endocytotic transport vesicle
Comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
lipid droplet (GO:0005811)
Namespace: cellular_component
Definition: An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
Synonyms: adiposome; lipid body; lipid particle
Comment: Note that this term does not refer to vesicles, but instead to structures in which lipids do not necessarily form bilayers.
centrosome (GO:0005813)
Namespace: cellular_component
Definition: A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
centriole (GO:0005814)
Namespace: cellular_component
Definition: A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
Synonyms: daughter centriole; mother centriole
Comment: In most eukaryotic cells, 'ciliary basal body' (GO:0036064) and 'centriole' (GO:0005814) represent a common entity that cycles through its function in cell division, then ciliogenesis, then cell division again. However, these structures are modified extensively as they transition into each other, and may contain different proteins, specific to each component.
microtubule organizing center (GO:0005815)
Namespace: cellular_component
Definition: An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
Synonyms: microtubule organising centre; MTOC
spindle pole body (GO:0005816)
Namespace: cellular_component
Definition: The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.
Synonyms: SPB
spindle (GO:0005819)
Namespace: cellular_component
Definition: The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
intermediate layer of spindle pole body (GO:0005821)
Namespace: cellular_component
Definition: Structure between the central and outer plaques of the spindle pole body.
inner plaque of spindle pole body (GO:0005822)
Namespace: cellular_component
Definition: One of three laminate structures that form the spindle pole body; the inner plaque is in the nucleus.
central plaque of spindle pole body (GO:0005823)
Namespace: cellular_component
Definition: One of three laminate structures that form the spindle pole body; the central plaque is embedded in the nuclear envelope.
half bridge of spindle pole body (GO:0005825)
Namespace: cellular_component
Definition: Structure adjacent to the plaques of the spindle pole body.
actomyosin contractile ring (GO:0005826)
Namespace: cellular_component
Definition: A cytoskeletal structure composed of actin filaments and myosin that forms beneath the plasma membrane of many cells, including animal cells and yeast cells, in a plane perpendicular to the axis of the spindle, i.e. the cell division plane. In animal cells, the contractile ring is located at the cleavage furrow. In budding fungal cells, e.g. mitotic S. cerevisiae cells, the contractile ring forms at the mother-bud neck before mitosis.
Synonyms: actomyosin ring; CAR; constriction ring; contractile actomyosin ring; cytokinetic ring
polar microtubule (GO:0005827)
Namespace: cellular_component
Definition: Any of the spindle microtubules that come from each pole and overlap at the spindle midzone. This interdigitating structure consisting of antiparallel microtubules is responsible for pushing the poles of the spindle apart.
Synonyms: pole-to-pole microtubule
kinetochore microtubule (GO:0005828)
Namespace: cellular_component
Definition: Any of the spindle microtubules that attach to the kinetochores of chromosomes by their plus ends, and maneuver the chromosomes during mitotic or meiotic chromosome segregation.
Synonyms: pole-to-kinetochore microtubule
cytosol (GO:0005829)
Namespace: cellular_component
Definition: The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
steroid hormone aporeceptor complex (GO:0005831)
Namespace: cellular_component
Definition: A protein complex consisting of a steroid receptor associated with nonreceptor proteins, minimally a dimer of Hsp90 and a monomer of hsp56/FKBP59; forms in the absence of bound ligand.
chaperonin-containing T-complex (GO:0005832)
Namespace: cellular_component
Definition: A multisubunit ring-shaped complex that mediates protein folding in the cytosol without a cofactor.
Synonyms: CCT particle; TriC
hemoglobin complex (GO:0005833)
Namespace: cellular_component
Definition: An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.
Synonyms: haemoglobin complex
heterotrimeric G-protein complex (GO:0005834)
Namespace: cellular_component
Definition: Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G protein-coupled receptors to an effector protein.
Synonyms: heterotrimeric G-protein GTPase activity; heterotrimeric G-protein GTPase, alpha-subunit; heterotrimeric G-protein GTPase, beta-subunit; heterotrimeric G-protein GTPase, gamma-subunit
Comment: See also the molecular function term 'G protein-coupled receptor activity ; GO:0004930'.
fatty acid synthase complex (GO:0005835)
Namespace: cellular_component
Definition: A multienzyme complex that catalyses the synthesis of fatty acids from acetyl CoA.
Synonyms: cytosolic FAS complex; cytosolic fatty acid synthase complex; cytosolic type I FAS complex; cytosolic type I fatty acid synthase complex; FAS complex; fatty acid synthetase complex; holo-[acyl-carrier-protein] synthase complex
fatty-acyl-CoA synthase complex (GO:0005836)
Namespace: cellular_component
Definition: A protein complex that possesses fatty-acyl-CoA synthase activity.
Synonyms: fatty acyl CoA synthase complex
Comment: Note that fatty acid synthetases of vertebrates and yeast are stable enzyme complexes of multifunctional polypeptide chains, whereas the fatty acid synthetases of plants and E. coli consist of non-associated individual enzymes.
obsolete 26S proteasome (GO:0005837)
Namespace: cellular_component
Definition: OBSOLETE. A large multisubunit protease found in the cytosol that recognizes, unfolds, and digests protein substrates that have been marked for degradation by the attachment of a ubiquitin group. Individual subcomplexes of the complete 26S proteasome are involved in these different tasks: the ATP-dependent 19S caps are believed to unfold substrates and feed them to the actual protease, the 20S proteasome.
Synonyms: 26S proteasome
Comment: This term was made obsolete because its definition was inaccurate.
proteasome regulatory particle (GO:0005838)
Namespace: cellular_component
Definition: A multisubunit complex, which caps one or both ends of the proteasome core complex. This complex recognizes and unfolds ubiquitinated proteins, and translocates them to the proteasome core complex.
Synonyms: 19S regulatory particle; modulator complex; PA700 proteasome activator; PA700-dependent proteasome activator
proteasome core complex (GO:0005839)
Namespace: cellular_component
Definition: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.
Synonyms: 20S core complex; 20S proteasome; macropain; PA28gamma-20S proteasome
ribosome (GO:0005840)
Namespace: cellular_component
Definition: An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
Synonyms: free ribosome; membrane bound ribosome; ribosomal RNA
obsolete polysome (GO:0005844)
Namespace: cellular_component
Definition: OBSOLETE. A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.
Synonyms: polyribosome
Comment: The reason for obsoletion is that the term is out of scope for GO.
obsolete mRNA cap binding complex (GO:0005845)
Namespace: cellular_component
Definition: OBSOLETE. Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)
Namespace: cellular_component
Definition: 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.
Synonyms: CFII complex; cleavage and polyadenylylation specificity factor activity; CPF complex; CPSF complex
mRNA cleavage stimulating factor complex (GO:0005848)
Namespace: cellular_component
Definition: A protein complex required for mRNA cleavage but not for poly(A) addition.
Synonyms: cleavage stimulation factor activity; CstF complex
eukaryotic translation initiation factor 2 complex (GO:0005850)
Namespace: cellular_component
Definition: Complex of three heterogeneous polypeptide chains, that form a ternary complex with initiator methionyl-tRNA and GTP. This ternary complex binds to free 40S subunit, which subsequently binds the 5' end of mRNA.
Synonyms: eIF-2; eIF2
eukaryotic translation initiation factor 3 complex (GO:0005852)
Namespace: cellular_component
Definition: A complex of several polypeptides that plays at least two important roles in protein synthesis: First, eIF3 binds to the 40S ribosome and facilitates loading of the Met-tRNA/eIF2.GTP ternary complex to form the 43S preinitiation complex. Subsequently, eIF3 apparently assists eIF4 in recruiting mRNAs to the 43S complex. The eIF3 complex contains five conserved core subunits, and may contain several additional proteins; the non-core subunits are thought to mediate association of the complex with specific sets of mRNAs.
Synonyms: eIF-3; eIF3
eukaryotic translation elongation factor 1 complex (GO:0005853)
Namespace: cellular_component
Definition: A multisubunit nucleotide exchange complex that binds GTP and aminoacyl-tRNAs, and catalyzes their codon-dependent placement at the A-site of the ribosome. In humans, the complex is composed of four subunits, alpha, beta, delta and gamma.
nascent polypeptide-associated complex (GO:0005854)
Namespace: cellular_component
Definition: A heterodimeric protein complex that can reversibly bind to ribosomes, and is located in direct proximity to newly synthesized polypeptide chains as they emerge from the ribosome.
Synonyms: NAC; NACA
muscle myosin complex (GO:0005859)
Namespace: cellular_component
Definition: A filament of myosin found in a muscle cell of any type.
troponin complex (GO:0005861)
Namespace: cellular_component
Definition: A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction.
striated muscle myosin thick filament (GO:0005863)
Namespace: cellular_component
Definition: Bipolar filaments formed of polymers of a muscle-specific myosin II isoform, found in the middle of sarcomeres in myofibrils.
striated muscle thin filament (GO:0005865)
Namespace: cellular_component
Definition: Filaments formed of actin and associated proteins; attached to Z discs at either end of sarcomeres in myofibrils.