Go terms map to parent GO term: GO:0005622   other intracellular
GOID
Link to GO
 Functional Category Description Protein Count
link to
protein list
GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. 7610
GO:0005737 cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 1733
GO:0005802 trans-Golgi network The network of interconnected tubular and cisternal structures located at the side of the Golgi apparatus 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. 1313
GO:0043231 intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. 961
GO:0044446 intracellular organelle part A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. 794
GO:0043232 intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. 398
GO:0009579 thylakoid A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation. 318
GO:0030529 ribonucleoprotein complex A macromolecular complex containing both protein and RNA molecules. 237
GO:0005929 cilium A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. 226
GO:0044424 intracellular part Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. 193
GO:0005844 polysome Several ribosomes bound to one mRNA. 184
GO:0080008 Cul4-RING ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein. 182
GO:0000131 incipient cellular bud site The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence. 174
GO:0005856 cytoskeleton Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. 143
GO:0005700 polytene chromosome A type of chromosome in a polyploid cell, formed when multiple copies of homologous chromosomes are aligned side by side to give a giant chromosome in which distinct chromosome bands are readily visible. 142
GO:0008540 proteasome regulatory particle, base subcomplex The subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex. 138
GO:0000785 chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. 128
GO:0000151 ubiquitin ligase complex A protein complex that includes a ubiquitin-protein ligase and other proteins that may confer substrate specificity on the complex. 127
GO:0005801 cis-Golgi network The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum. 121
GO:0030686 90S preribosome A large ribonucleoprotein complex considered to be the earliest preribosomal complex. In S. cerevisiae, it has a size of 90S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins. 116
GO:0000159 protein phosphatase type 2A complex A protein complex that has protein serine/threonine phosphatase activity that is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone H1; it constitutes a subclass of several enzymes activated by different histones and polylysine, and consists of catalytic, scaffolding, and regulatory subunits. The catalytic and scaffolding subunits form the core enzyme, and the holoenzyme also includes the regulatory subunit. 115
GO:0019005 SCF ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1). 114
GO:0032588 trans-Golgi network membrane The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network. 113
GO:0005657 replication fork The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. 110
GO:0000775 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. 108
GO:0033503 HULC complex A ubiquitin-conjugating enzyme complex that contains two RING finger proteins, which have ubiquitin ligase activity, in addition to a protein with ubiquitin-conjugating enzyme activity; catalyzes the ubiquitination of histone H2B at lysine 119 (or the equivalent residue). In Schizosaccharomyces the subunits are Rhp1, Brl2/Rfp1 and Brl1/Rfp2. 107
GO:0030687 preribosome, large subunit precursor A preribosomal complex consisting of 27SA, 27SB, and/or 7S pre-rRNA, 5S rRNA, ribosomal proteins including late-associating large subunit proteins, and associated proteins; a precursor of the eukaryotic cytoplasmic large ribosomal subunit. 104
GO:0000502 proteasome complex A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core. 102
GO:0043590 bacterial nucleoid The region of a bacterial cell to which the DNA is confined. 102
GO:0031967 organelle envelope A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. 100
GO:0044427 chromosomal part Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. 94
GO:0001741 XY body A structure found in a male mammalian spermatocyte containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery. 92
GO:0005694 chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. 91
GO:0031513 nonmotile primary cilium A primary cilium which contains a variable array of axonemal microtubules but does not contain molecular motors. Nonmotile primary cilia are found on many different cell types and function as sensory organelles that concentrate and organize sensory signaling molecules. 90
GO:0005954 calcium- and calmodulin-dependent protein kinase complex An enzyme complex which in eukaryotes is composed of four different chains: alpha, beta, gamma, and delta. The different isoforms assemble into homo- or heteromultimeric holoenzymes composed of 8 to 12 subunits. Catalyzes the phosphorylation of proteins to O-phosphoproteins. 86
GO:0030289 protein phosphatase 4 complex The complex formed by the catalytic subunit of protein phosphatase 4 plus a regulatory subunit. 83
GO:0016235 aggresome An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules. 83
GO:0005834 heterotrimeric G-protein complex 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. 81
GO:0031372 UBC13-MMS2 complex A heterodimeric ubiquitin conjugating enzyme complex that catalyzes assembly of K63-linked polyubiquitin chains, which act as a signal to promote error-free DNA postreplication repair; in Saccharomyces the complex comprises Ubc13p and Mms2p. 72
GO:0035370 UBC13-UEV1A complex A heterodimeric ubiquitin conjugating enzyme complex that catalyzes assembly of K63-linked polyubiquitin chains and is involved in NF-kappaB activation. In humans at least, the complex comprises the ubiquitin-conjugating enzyme UBC13 and ubiquitin-conjugating enzyme variant 1A (UEV1A). 71
GO:0032391 photoreceptor connecting cilium A nonmotile primary cilium that has a 9+0 microtubule array and forms the portion of the axoneme traversing the boundary between the photoreceptor inner and outer segments. 71
GO:0043229 intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. 69
GO:0070732 spindle envelope An organelle envelope that surrounds the chromosomes and the central part of the spindle apparatus during mitosis and meiosis; observed in many invertebrates. The spindle envelope consists of membrane layers, called parafusorial membranes, derived from endoplasmic reticulum membrane; in male meiosis it forms during prometaphase and persists until early in the ensuing interphase. 69
GO:0032040 small-subunit processome A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins. 67
GO:0005703 polytene chromosome puff A swelling at a site along the length of a polytene chromosome, thought to be the site of active transcription. 59
GO:0000781 chromosome, telomeric region The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. 57
GO:0000307 cyclin-dependent protein kinase holoenzyme complex Cyclin-dependent protein kinases (CDKs) are heterodimeric enzymes that contain a kinase catalytic subunit associated with a regulatory cyclin partner. 57
GO:0016442 RNA-induced silencing complex A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation. 54
GO:0000793 condensed chromosome A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure. 54
GO:0005732 small nucleolar ribonucleoprotein complex A ribonucleoprotein complex that contains an RNA molecule of the small nucleolar RNA (snoRNA) family and associated proteins. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type. 54
GO:0000776 kinetochore A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules. 50
GO:0010168 ER body A novel compartment found in plant cells that is derived from the ER. The structures have a characteristic shape and size (10 mm long and 0.5 mm wide) and are surrounded with ribosomes. They have been found in Arabidopsis thaliana and related Brassicaceae species. 49
GO:0019774 proteasome core complex, beta-subunit complex The proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex. An example of this component is found in Mus musculus. 41
GO:0070013 intracellular organelle lumen An organelle lumen that is part of an intracellular organelle. 37
GO:0031514 motile cilium A cilium which has a variable arrangement of axonemal microtubules, contains molecular motors, and beats with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia are typically found in multiple copies on epithelial cells that line the lumenal ducts of various tissues. Motile cilia may also function as sensory organelles. 37
GO:0001520 outer dense fiber Structure or material found in the flagella of mammalian sperm that surrounds each of the nine microtubule doublets, giving a 9 + 9 + 2 arrangement rather than the 9 + 2 pattern usually seen. These dense fibers are stiff and noncontractile. 35
GO:0000940 condensed chromosome outer kinetochore The region of a condensed chromosome kinetochore most external to centromeric DNA; this outer region mediates kinetochore-microtubule interactions. 35
GO:0022623 proteasome-activating nucleotidase complex A multisubunit complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner. 33
GO:0005704 polytene chromosome band A stretch of densely packed chromatin along the polytene chromosome, visible as a morphologically distinct band. 32
GO:0005705 polytene chromosome interband A stretch of less tightly packed chromatin along the polytene chromosome, found between bands. 31
GO:0035068 micro-ribonucleoprotein complex A complex containing both protein and micro-RNA (miRNA) molecules. miRNAs are approximately 22 nucleotide noncoding RNAs derived from endogenous genes; they are processed from the stem of a longer hairpin like structure termed a pre-miRNA. 31
GO:0031934 mating-type region heterochromatin Heterochromatic regions of the chromosome found at silenced mating-type loci. 30
GO:0031523 Myb complex A multisubunit complex consisting of Myb and other proteins that regulates site specific DNA replication, gene amplification and transcriptional repression. 30
GO:0005845 mRNA cap binding complex Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA. 28
GO:0000792 heterochromatin A compact and highly condensed form of chromatin. 28
GO:0019773 proteasome core complex, alpha-subunit complex The proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex. An example of this component is found in Mus musculus. 28
GO:0016234 inclusion body A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers. 27
GO:0035770 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. 27
GO:0031463 Cul3-RING ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul3 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a BTB-domain-containing protein. 26
GO:0035327 transcriptionally active chromatin The ordered and organized complex of DNA and protein that forms regions of the chromosome that are being actively transcribed. 26
GO:0031588 AMP-activated protein kinase complex A protein complex that possesses AMP-dependent protein kinase activity. 26
GO:0042622 photoreceptor outer segment membrane The membrane surrounding the outer segment of a vertebrate photoreceptor. 25
GO:0033551 monopolin complex A protein complex required for clamping microtubule binding sites, ensuring orientation of sister kinetochores to the same pole (mono-orientation) during meiosis I. In the yeast S. cerevisiae this complex consists of Csm1p, Lrs4p, Hrr25p and Mam1p; in S. pombe Psc1 and Mde4 have been identified as subunits. 25
GO:0072372 primary cilium A cilium found on many different cell types that is typically present in a single copy per cell. A primary cilium may have a variable array of axonemal microtubules and may or may not contain molecular motors. 24
GO:0005952 cAMP-dependent protein kinase complex An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer. 23
GO:0060170 cilium membrane The portion of the plasma membrane surrounding a cilium. 22
GO:0035861 site of double-strand break A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. 21
GO:0031462 Cul2-RING ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul2 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein. 20
GO:0008541 proteasome regulatory particle, lid subcomplex The subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex. 20
GO:0031932 TORC2 complex A protein complex that contains at least TOR (target of rapamycin) and Rictor (rapamycin-insensitive companion of TOR), or orthologs of, in complex with other signaling components. Mediates the phosphorylation and activation of PKB (also called AKT). In Saccharomyces, the complex contains Avo1p, Avo2p, Tsc11p, Lst8p, Bit61p, Slm1p, Slm2p, and Tor2p. 20
GO:0032420 stereocilium An actin-based protrusion from the apical surface of auditory and vestibular hair cells. Bundles of stereocilia act as mechanosensory organelles. 19
GO:0005956 protein kinase CK2 complex A protein complex that possesses protein serine/threonine kinase activity, and contains two catalytic alpha subunits and two regulatory beta subunits. Protein kinase CK2 complexes are found in nearly every subcellular compartment, and can phosphorylate many protein substrates in addition to casein. 19
GO:0017101 aminoacyl-tRNA synthetase multienzyme complex A multienzyme complex found in all multicellular eukaryotes composed of eight proteins with aminoacyl-tRNA synthetase activities (abbreviated as: ArgRS, AspRS, GluProRS, GlnRS, IleRS, LeuRS, LysRS, MetRS where RS is the enzyme, preceded by the amino acid it uses as a substrate) as well as three non-synthetase proteins (p43, p38, and p18) with diverse functions. Several of these subunits are known dimers, so the total polypeptide count in the multisynthetase complex is at least fifteen. All of the enzymes in this assembly catalyze the same reaction, the covalent attachment of an amino acid to either the 2'- or 3'-hydroxyl of the 3'-terminal adenosine of tRNA, but using different substrates. 19
GO:0031464 Cul4A-RING ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul4A subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein. 18
GO:0031931 TORC1 complex A protein complex that contains at least TOR (target of rapamycin) and Raptor (regulatory-associated protein of TOR), or orthologs of, in complex with other signaling components. Mediates the phosphorylation and activation of S6K. In Saccharomyces, the complex contains Kog1p, Lst8p, Tco89p, and either Tor1p or Tor2p. 18
GO:0031301 integral to organelle membrane Penetrating at least one phospholipid bilayer of an organelle membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. 18
GO:0000806 Y chromosome The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males. 18
GO:0000939 condensed chromosome inner kinetochore The region of a condensed chromosome kinetochore closest to centromeric DNA; in mammals the CREST antigens (CENP proteins) are found in this layer; this layer may help define underlying centromeric chromatin structure and position of the kinetochore on the chromosome. 17
GO:0010170 glucose-1-phosphate adenylyltransferase complex Complex that catalyzes the synthesis of ADP-glucose and pyrophosphate from glucose-1-phosphate and ATP. In plants, the complex is a heterotetramer composed of two types of subunits (small and large). In bacteria, the enzyme complex is composed of four identical subunits. 17
GO:0005663 DNA replication factor C complex A complex of five polypeptides in eukaryotes, and two in prokaryotes, that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. 16
GO:0005721 centromeric heterochromatin A region of heterochromatin located near the centromere of a chromosome. 16
GO:0000178 exosome (RNase complex) Complex of 3'-5' exoribonucleases. 15
GO:0000805 X chromosome The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males. 15
GO:0031933 telomeric heterochromatin Heterochromatic regions of the chromosome found at the telomeres. 15
GO:0043505 centromere-specific nucleosome A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3). 15
GO:0031234 extrinsic to internal side of plasma membrane Loosely bound to the surface of the plasma membrane that faces the cytoplasm, but not integrated into the hydrophobic region. 14
GO:0010598 NAD(P)H dehydrogenase complex (plastoquinone) Complex that possesses NAD(P)H dehydrogenase (plastoquinone) activity. The complex is one of the components of the electron transport chain. It is involved in electron transport from an unidentified electron donor, possibly NADH, NADPH or ferredoxin(Fd) to the plastoquinone pool. 13
GO:0036126 sperm flagellum A microtubule-based flagellum that is part of a sperm, a mature male germ cell that develops from a spermatid. 13
GO:0030014 CCR4-NOT complex The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins. 13
GO:0031391 Elg1 RFC-like complex A pentameric complex related to replication factor C, which loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA and has roles in telomere length regulation and other aspects of genome stability. In Saccharomyces the subunits are known as Elg1p, Rfc2p, Rfc3p, Rfc4p, and Rfc5p. 13
GO:0030684 preribosome Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis. 13
GO:0031389 Rad17 RFC-like complex A pentameric protein complex related to replication factor C, which loads a trimeric complex of checkpoint proteins (known as the checkpoint clamp or 9-1-1 complex) onto DNA at damage sites; functions in DNA damage cell cycle checkpoints. In Schizosaccharomyces pombe the subunits are known as Rad17, Rfc2, Rfc3, Rfc4, and Rfc5, while in Saccharomyces cerevisiae the subunits are known as Rad24p, Rfc2p, Rfc3p, Rfc4p, and Rfc5p. 13
GO:0001750 photoreceptor outer segment The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes. 12
GO:0022624 proteasome accessory complex A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex. 12
GO:0031095 platelet dense tubular network membrane The lipid bilayer surrounding the platelet dense tubular network. 12
GO:0005955 calcineurin complex A heterodimeric calcium ion and calmodulin dependent protein phosphatase composed of catalytic and regulatory subunits; the regulatory subunit is very similar in sequence to calmodulin. 12
GO:0033106 cis-Golgi network membrane The lipid bilayer surrounding any of the compartments that make up the cis-Golgi network. 11
GO:0031390 Ctf18 RFC-like complex A heptameric complex related to replication factor C, which loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA and plays a vital role in chromosome cohesion. In Saccharomyces the subunits are known as Ctf18p, Rfc2p, Rfc3p, Rfc4p, Rfc5p, Dcc1p, and Ctf8p. 11
GO:0097226 sperm mitochondrial sheath The tightly packed helical sheath of ATP-producing mitochondria restricted to the midpiece of the sperm flagellum. 11
GO:0030076 light-harvesting complex A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center. 11
GO:0005727 extrachromosomal circular DNA Circular DNA structures that are not part of a chromosome. 11
GO:0010369 chromocenter A region in which centric, heterochromatic portions of one or more chromosomes form a compact structure. 10
GO:0033256 I-kappaB/NF-kappaB complex A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. 10
GO:0030008 TRAPP complex A large complex that acts as a tethering factor involved in transporting vesicles from the ER through the Golgi to the plasma membrane. A TRAPP (transport protein particle) complex has a core set of proteins which are joined by specific subunits depending on the cellular component where a given TRAPP complex is active. 9
GO:0048269 methionine adenosyltransferase complex A multimeric enzyme complex composed of variable numbers of catalytic alpha subunits, and noncatalytic beta subunits. The beta subunits are believed to have a regulatory function. The enzyme complex catalyzes the synthesis of S-adenosylmethionine (AdoMet), which is the major methyl group donor, participating in the methylation of proteins, DNA, RNA, phospholipids, and other small molecules. 9
GO:0000786 nucleosome A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. 9
GO:0009330 DNA topoisomerase complex (ATP-hydrolyzing) Complex that possesses DNA topoisomerase (ATP-hydrolyzing) activity. 9
GO:0043494 CLRC ubiquitin ligase complex An active cullin-dependent E3 ubiquitin ligase complex essential for heterochromatin assembly by RNAi and histone H3K9 methylation. 9
GO:0045260 plasma membrane proton-transporting ATP synthase complex A proton-transporting ATP synthase complex found in the plasma membrane. Examples of this component are found in Bacterial species. 9
GO:0070761 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. 8
GO:0031511 Mis6-Sim4 complex A protein complex that forms part of the inner centromere, which is involved in the loading of the centromeric histone h3 variant CENP-A onto centromeres and in centromere specific heterochromatin formation. The complex contains about 12 proteins, of which two are known as Mis6 and Sim4 in S. pombe and CENP-I and CENP-H in human. 8
GO:0045282 plasma membrane succinate dehydrogenase complex A multimeric complex which consists of flavoprotein (subunit A ; InterPro:IPR003952), iron-sulfur protein (subunit B) and membrane-bound cytochrome b560 (subunit C; InterPro:IPR000701). In some Archaea, the membrane-bound subunits (C or C and D) do not necessarily contain heme. Membrane-bound subunits can bind/react with quinones. Examples of this component are found in Bacterial species. 8
GO:0030894 replisome A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins. 8
GO:0034657 GID complex A protein complex with ubiquitin ligase activity that is involved in proteasomal degradation of fructose-1,6-bisphosphatase (FBPase) and phosphoenolpyruvate carboxykinase during the transition from gluconeogenic to glycolytic growth conditions. In S. cerevisiae, the GID (Glucose Induced degradation Deficient) complex consists of Vid30p, Rmd5p, Vid24p, Vid28p, Gid7p, Gid8p, and Fyv10p. 7
GO:0017117 single-stranded DNA-dependent ATP-dependent DNA helicase complex A protein complex that possesses single-stranded DNA-dependent DNA helicase activity. 7
GO:0000791 euchromatin A dispersed and relatively uncompacted form of chromatin. 7
GO:0000779 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. 6
GO:0031461 cullin-RING ubiquitin ligase complex Any ubiquitin ligase complex in which the catalytic core consists of a member of the cullin family and a RING domain protein; the core is associated with one or more additional proteins that confer substrate specificity. 6
GO:0030688 preribosome, small subunit precursor A preribosomal complex consisting of 20S pre-rRNA, ribosomal proteins including late-associating small subunit proteins, and associated proteins; a precursor of the eukaryotic cytoplasmic small ribosomal subunit. 6
GO:0033588 Elongator holoenzyme complex A heterohexameric protein complex that is involved in modification of wobble nucleosides in tRNA, and exerts direct effects on transcriptional elongation and exocytosis. The complex can associate physically with hyperphosphorylated RNA polymerase II; it contains two discrete heterotrimeric subcomplexes. 6
GO:0030956 glutamyl-tRNA(Gln) amidotransferase complex A protein complex that possesses glutamyl-tRNA(Gln) amidotransferase activity, and therefore creates Gln-tRNA by amidating Glu-tRNA; usually composed of 3 subunits: A, B, and C. Note that the C subunit may not be required in all organisms. 6
GO:0035657 eRF1 methyltransferase complex A protein complex required for the methylation of a glutamine (Gln) residue in the protein release factor eRF1. In S. cerevisiae, this complex consists of at least Trm112p and Mtq2p. 6
GO:0033185 dolichol-phosphate-mannose synthase complex A protein complex that possesses dolichyl-phosphate beta-D-mannosyltransferase activity; contains a catalytic subunit, a regulatory subunit, and a third subunit that stabilizes the complex. In human and several other metazoa, the subunits are named DPM1, DPM2 and DPM3, respectively. 5
GO:0032299 ribonuclease H2 complex A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p. 5
GO:0070419 nonhomologous end joining complex A protein complex that plays a role in DNA double-strand break repair via nonhomologous end joining. Such complexes typically contain a specialized DNA ligase (e.g. Lig4 in eukaryotes) and one or more proteins that bind to DNA ends. 5
GO:0031465 Cul4B-RING ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul4B subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by unknown subunits. 5
GO:0045252 oxoglutarate dehydrogenase complex A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) ; EC:1.2.4.2 (E1), dihydrolipoamide S-succinyltransferase ; EC:2.3.1.61 (E2) and dihydrolipoamide dehydrogenase ; EC:1.8.1.4 (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2). 4
GO:0045262 plasma membrane proton-transporting ATP synthase complex, catalytic core F(1) The catalytic sector of the plasma membrane hydrogen-transporting ATP synthase; it comprises the catalytic core and central stalk, and is peripherally associated with the plasma membrane when the entire ATP synthase is assembled. Examples of this component are found in Bacterial species. 4
GO:0031371 ubiquitin conjugating enzyme complex Any complex that possesses ubiquitin conjugating enzyme activity. 4
GO:0009368 endopeptidase Clp complex A protein complex comprised of members of the ClpX, ClpC, ClpD, ClpP or ClpR protein families. ClpPs are the proteolytic subunit of active complexes, and ClpA and ClpX form the regulatory subunits. Enzymatically active and inactive complexes can form. 4
GO:0005953 CAAX-protein geranylgeranyltransferase complex A heterodimeric enzyme, composed of an alpha and a beta subunit. Participates in the post-translational C-terminal modification of several small GTPases, allowing their targeting to the membrane. 4
GO:0030915 Smc5-Smc6 complex A conserved complex that contains a heterodimer of SMC proteins (Smc5p and Smc6p, or homologs thereof) and several other proteins, and is involved in DNA repair and maintaining cell cycle arrest following DNA damage. In S. cerevisiae, this is an octameric complex called Mms21-Smc5-Smc6 complex, with at least five of its subunits conserved in fission yeast and humans. 3
GO:0005930 axoneme The bundle of microtubules and associated proteins that forms the core of cilia and flagella in eukaryotic cells and is responsible for their movements. 3
GO:0000777 condensed chromosome kinetochore A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules. 3
GO:0000796 condensin complex A multisubunit protein complex that plays a central role in chromosome condensation. 3
GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1) The sector of a hydrogen-transporting ATP synthase complex in which the catalytic activity resides; it comprises the catalytic core and central stalk, and is peripherally associated with a membrane, such as the plasma membrane or the mitochondrial inner membrane, when the entire ATP synthase is assembled. 3
GO:0019866 organelle inner membrane The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites. 3
GO:0033553 rDNA heterochromatin A region of heterochromatin located at the rDNA repeats in a chromosome. 3
GO:0032300 mismatch repair complex Any complex formed of proteins that act in mismatch repair. 3
GO:0030893 meiotic cohesin complex A cohesin complex that mediates sister chromatid cohesion during meiosis; has a subunit composition distinct from that of the mitotic cohesin complex. 3
GO:0000408 EKC/KEOPS complex A protein complex proposed to be involved in transcription as well as promoting telomere uncapping and telomere elongation. For example, in Saccharomyces cerevisiae the complex contains Bud32p, Kae1p, Gon7p, Cgi121p, and Pcc1p. 3
GO:0016035 zeta DNA polymerase complex A heterodimeric DNA polymerase complex that catalyzes error-prone DNA synthesis in contexts such as translesion synthesis and double-stranded break repair. First characterized in Saccharomyces, in which the subunits are Rev3p and Rev7p; a third protein, Rev1p, is often associated with the polymerase dimer. 3
GO:0031968 organelle outer membrane The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope. 2
GO:0031984 organelle subcompartment A compartment that consists of a lumen and an enclosing membrane, and is part of an organelle. 2
GO:0005838 proteasome regulatory particle 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. 2
GO:0031617 NMS complex A supercomplex formed by the association of two subcomplexes (known as MIND and Ndc80 in Schizosaccharomyces) with additional proteins at the kinetochores of condensed nuclear chromosomes. 2
GO:0009360 DNA polymerase III complex The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork. 2
GO:0032797 SMN complex A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus. 2
GO:0071146 SMAD3-SMAD4 protein complex A heteromeric SMAD protein complex that contains SMAD3 and SMAD4. 2
GO:0031466 Cul5-RING ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul5 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein. 2
GO:0000808 origin recognition complex A multisubunit complex that is located at the replication origins of a chromosome. 2
GO:0030015 CCR4-NOT core complex The core of the CCR4-NOT complex. In Saccharomyces the CCR4-NOT core complex comprises Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p. 2
GO:0002944 cyclin K-CDK12 complex A protein complex consisting of cyclin Kand cyclin-dependent kinase 12 (CDK12). Cyclins are characterized by periodicity in protein abundance throughout the cell cycle. Cyclin-dependent kinases represent a family of serine/threonine protein kinases that become active upon binding to a cyclin regulatory partner. 2
GO:0031262 Ndc80 complex A protein complex conserved among eukaryotes that forms part of the kinetochore and plays an essential role in forming stable kinetochore-microtubule attachments. The complex contains proteins known in several species, including budding and fission yeasts, as Ndc80p, Nuf2p, Spc24p, and Spc25p. In vertebrates it is part of the outer plate of the kinetochore. 1
GO:0010370 perinucleolar chromocenter A chromocenter adjacent to the nucleolus. 1
GO:0070438 mTOR-FKBP12-rapamycin complex A protein complex that contains the mTOR (mammalian target of rapamycin) serine/threonine kinase, the peptidyl-prolyl cis-trans isomerase FKBP12 (FKBP1A) and rapamycin (sirolimus). 1
GO:0031094 platelet dense tubular network A network of membrane-bounded compartments found in blood platelets, where they regulate platelet activation by sequestering or releasing calcium. The dense tubular network exists as thin elongated membranes in resting platelets, and undergoes a major ultrastructural change, to a rounded vesicular form, upon addition of thrombin. 1
GO:0031518 CBF3 complex A multisubunit protein complex that binds to centromeric DNA and initiates kinetochore assembly. In yeast, this complex consists of four subunits, namely Ctf13p, Skp1p, Cep3p and Cbf2p. 1
GO:0000172 ribonuclease MRP complex A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family, and cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication. 1
GO:0032045 guanyl-nucleotide exchange factor complex A protein complex that stimulates the exchange of guanyl nucleotides associated with a GTPase. 1
GO:0008278 cohesin complex A protein complex that is required for sister chromatid cohesion in eukaryotes. The cohesin complex forms a molecular ring complex, and is composed of structural maintenance of chromosomes (SMC) and kleisin proteins. For example, in yeast, the complex is composed of the SMC proteins Smc1p and Smc3p, and the kleisin protein Scc1p. In vertebrates, the complex is composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domains to a kleisin (RAD21, REC8 or RAD21L) which links them, and one STAG protein (STAG1, STAG2 or STAG3). 1
GO:0005839 proteasome core complex A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex. 1
GO:0008280 cohesin core heterodimer The core heterodimer of a cohesin complex; a structure required for sister chromatid cohesion in eukaryotes. 1
GO:0008043 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. 1
GO:0097228 sperm principal piece The segment of the sperm flagellum where the mitochondrial sheath ends, and the outer dense fibers (ODFs) associated with outer axonemal doublets 3 and 8 are replaced by the 2 longitudinal columns of the fibrous sheath (FS) which run the length of the principal piece and are stabilized by circumferential ribs. The principal piece makes up ~2/3 of the length of the sperm flagellum and is defined by the presence of the FS and of only 7 (rather than 9) ODFs which taper and then terminate near the distal end of the principal piece. 1
GO:0005846 nuclear cap binding complex A conserved heterodimeric protein complex that binds to the 5' terminal cap structure m7G(5')ppp(5')N of nascent eukaryotic RNA polymerase II transcripts such as pre-mRNA and U snRNA. The consists of proteins known as CBP20 and CBP80, binds to cap structures in the nucleus, and is involved in pre-mRNA splicing, 3'-end formation, and RNA nuclear export. 1
GO:0009379 Holliday junction helicase complex A DNA helicase complex that forms part of a Holliday junction resolvase complex, where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA. 1
GO:0043626 PCNA complex A protein complex composed of three identical PCNA monomers, each comprising two similar domains, which are joined in a head-to-tail arrangement to form a homotrimer. Forms a ring-like structure in solution, with a central hole sufficiently large to accommodate the double helix of DNA. Originally characterized as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the replisome, and has also been shown to be involved in other processes including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation. 1
GO:0035328 transcriptionally silent chromatin The ordered and organized complex of DNA and protein that forms regions of the chromosome that are not being actively transcribed. 1
GO:0045259 proton-transporting ATP synthase complex A proton-transporting two-sector ATPase complex that catalyzes the phosphorylation of ADP to ATP during oxidative phosphorylation. The complex comprises a membrane sector (F0) that carries out proton transport and a cytoplasmic compartment sector (F1) that catalyzes ATP synthesis by a rotational mechanism; the extramembrane sector (containing 3 a and 3 b subunits) is connected via the d-subunit to the membrane sector by several smaller subunits. Within this complex, the g and e subunits and the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis. This movement is driven by the hydrogen ion electrochemical potential gradient. 1