GO:0016580

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Sin3 complex

A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.

SIN3B, NCOR1, RBBP4, HDAC1, HDAC2, PHF12, SUDS3, FAM60A, MORF4L1

GO:0016581

CC

NuRD complex

An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.

MBD3, RBBP4, HDAC1, CHD4, GATAD2A, APPL2, HDAC2

GO:0016589

CC

NURF complex

An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters.

SMARCA5, SMARCA1, RBBP4, BAP18, HMGXB4

GO:0016590

CC

ACF complex

An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and generally no other subunits, though Xenopus is an exception with a third non-conserved subunit. ACF plays roles in regulation of RNA polymerase II transcription and in DNA replication and repair.

BAZ1A

GO:0016591

CC

DNA-directed RNA polymerase II, holoenzyme

Large protein complex composed of the RNA polymerase core complex and a variety of other proteins including transcription factor complexes TFIIA, D, E, F, and H which are required for promoter recognition, and the Mediator subcomplex. Catalyzes the synthesis of eukaryotic pre-mRNA.

RPRD1A, MYO6

GO:0016592

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mediator complex

A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.

MED19, MED7, MED14, MED6, GLI3, CDK8, MED21, PPARGC1B, MED12, MED30, MED15, MED20, MED4, MED17, MED9, THRAP3, MED16

GO:0016593

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Cdc73/Paf1 complex

A multiprotein complex that associates with RNA polymerase II and general RNA polymerase II transcription factor complexes and may be involved in both transcriptional initiation and elongation. In Saccharomyces the complex contains Paf1p, Cdc73p, Ctr9p, Rtf1p, and Leo1p.

RTF1

GO:0016600

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flotillin complex

A protein complex that contains flotillin-1 and flotillin-2, and may contain associated proteins. Flotillins associate into membrane microdomains resembling caveolae.

FLOT1, CTNNA1, CTNNB1, CORO1C

GO:0016602

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CCAAT-binding factor complex

A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5.

NFYB, NFYC

GO:0016604

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nuclear body

Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.

TP53, SKI, MDM2, ZBTB16, ZFHX3, MSANTD1, MTDH, CREBRF, GEMIN5, GEMIN6, CREBBP, TOLLIP, HIPK2, NCOR2

GO:0016605

CC

PML body

A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.

ARNTL, DAPK3, NBN, N4BP1, TDP2, TP53, RB1, SKI, SP100, CBX5, ATRX, MRE11A, BLM, HIRA, SUMO3, PTEN, SUMO2, UBE2I, SATB1, SP3, ZBTB16, RAD51, MAPK7, SQSTM1, TDG, MORC3, RFWD3, TP53INP2, SMC5, TOPBP1, KAT6A, TP53INP1, ISG20, SMC6, TRIM8, SPTBN4, HIPK2, MKNK2, TCF7L2, EIF4ENIF1, THAP1, PPARGC1A, ZMYM2, RNF6, ZNF451

GO:0016607

CC

nuclear speck

A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.

APBB1, SAP18, DDX3X, PRPF3, PPIH, PLRG1, PQBP1, DUSP11, PRPF40A, SRSF10, LUC7L3, CD2BP2, LMNA, GLI2, GLI3, PSKH1, PRKACA, SON, WT1, PPP1CC, NRIP1, CSNK1A1, RBM25, CLK2, AFF2, SRP54, SARNP, SRSF2, ZBTB16, MEF2C, RING1, SRSF1, SF3A3, TARDBP, SRSF5, SRSF6, PPIG, CDK13, RBM39, ZNF638, PSME4, WTAP, SART3, NONO, RNPS1, HIF1A, IFI16, TIMM50, FAM76B, ZC3H13, ARL6IP4, THOC7, ALKBH5, ZC3H14, CBLL1, DDX46, PABPN1, ALYREF, TRIM69, GATAD2A, SRRM1, TRIM22, KMT2E, MAML2, AGGF1, THOC2, PNISR, ATXN2L, PRPF31, PSPC1, RSRC1, THOC3, EAF1, MAML3, YTHDC1, CCNL2, SMC6, ATOH8, RBM15, CDC5L, PRPF18, EPAS1, WAC, RBM4, POLDIP3, CRNKL1, FTO, PNN, NEK6, CWC22, PLCB1, EIF4ENIF1, GPATCH2, BCLAF1, CDK12, NXF1, CCNL1, NXT1, ZMIZ1, PRPF19, SRRM2, HIF3A, THRAP3, LUC7L2, RBM8A

GO:0016935

CC

glycine-gated chloride channel complex

A protein complex that forms a transmembrane channel through which chloride ions may pass in response to glycine binding to the channel complex or one of its constituent parts.

GLRB

GO:0016939

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kinesin II complex

A complex consisting of two distinct motor subunits that form a heterodimer complexed with a third non-motor accessory subunit, the kinesin associated protein or KAP; the KIF3 heterodimer interacts via its C-terminal portion with KAP, which is thought to regulate the binding of the motor to cargo membranes.

KIFAP3, KIF3A

GO:0016942

CC

insulin-like growth factor binding protein complex

A complex of proteins which includes the insulin-like growth factor (IGF) and a number of IGF-binding proteins. The complex plays a role in growth and development.

IGF1, IGFBP3, IGFBP5

GO:0017053

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transcriptional repressor complex

A protein complex that possesses activity that prevents or downregulates transcription.

HDAC3, TBL1X, NCOR1, JUN, HMGB1, GLI3, SKI, SKIL, YWHAB, CBX5, HDGF, HDAC4, CTBP2, INSM1, SP3, ZBTB16, GPS2, C1D, DEPDC1, JAZF1, SMARCC2, N4BP2L2, CORO2A, LIN37, PHF12, SPEN, TBL1XR1, ZNF350, RLIM, ZNF224, RCOR3, NCOR2

GO:0017059

CC

serine C-palmitoyltransferase complex

An enzyme complex that catalyzes the transfer of a palmitoyl on to serine, forming 3-dehydro-D-sphinganine.

SPTLC2, SPTSSB

GO:0017101

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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.

EPRS, RARS, KARS

GO:0017109

CC

glutamate-cysteine ligase complex

An enzyme complex that catalyzes the ligation of glutamate to cysteine, forming glutamylcysteine.

GCLC, GCLM

GO:0017119

CC

Golgi transport complex

A multisubunit tethering complex of the CATCHR family (complexes associated with tethering containing helical rods) that has a role in tethering vesicles to the Golgi prior to fusion. In yeast, this complex is called the Sec34/35 complex and is composed of eight subunits (Sec34p, Sec35p, Dor1p, Cod1p, Cod2p, Cod3p, Cod4p, and Cod5p). In mammals the subunits are named COG1-8.

COG2, COG6

GO:0017146

CC

NMDA selective glutamate receptor complex

An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. NMDA receptors are composed of assemblies of NR1 subunits (Figure 3) and NR2 subunits, which can be one of four separate gene products (NR2A-D). Expression of both subunits are required to form functional channels. The glutamate binding domain is formed at the junction of NR1 and NR2 subunits. NMDA receptors are permeable to calcium ions as well as being permeable to other ions. Thus NMDA receptor activation leads to a calcium influx into the post-synaptic cells, a signal thought to be crucial for the induction of NMDA-receptor dependent LTP and LTD.

GRIN2A, EPS8, NLGN1

GO:0017177

CC

glucosidase II complex

A heterodimeric complex that catalyzes the trimming of glucose residues from N-linked core glycans on newly synthesized glycoproteins.

GANAB

GO:0018444

CC

translation release factor complex

A heterodimeric complex involved in the release of a nascent polypeptide chain from a ribosome.

GSPT1

GO:0019005

CC

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).

CKS2, CCNF, CKS1B, RBX1, SKP1, SKP2, FBXO31, SPOPL, ABTB2, FBXO18, FBXO25, FBXO32, FBXW5, FBXO17, BTBD9, FBXL15, FBXO44, KBTBD4, FBXL7, FBXO9, FBXL2, BTRC, BTBD3

GO:0019031

CC

viral envelope

The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.

ERVW-1

GO:0019034

CC

viral replication complex

Specific locations and structures in the virus infected cell involved in replicating the viral genome.

FMR1

GO:0019035

CC

viral integration complex

A nucleoprotein complex containing viral genetic material and associated viral and host proteins, which is capable of inserting a viral genome into a host genome.

TOP2A

GO:0019185

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snRNA-activating protein complex

A protein complex that recognizes the proximal sequence element of RNA polymerase II and III snRNA promoters.

SNAPC1

GO:0019773

CC

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.

PSMA1, PSMA2, PSMA3, PSMA4

GO:0019774

CC

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.

PSMB3

GO:0019815

CC

B cell receptor complex

An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.

SYK

GO:0019867

CC

outer membrane

The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

ANKH

GO:0019897

CC

extrinsic component of plasma membrane

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

ANXA2, TDGF1, NUMB, S100A10, RAC1, FMR1, MFGE8, EEA1, AAK1, SCUBE1, SYTL2

GO:0019898

CC

extrinsic component of membrane

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

FRMD3, BCL2L11, SNX3, NMT2, FARP2, SNX4, ANXA1, PRNP, TPR, EZR, MAL, NF2, RDX, PLAUR, SNX1, WIPI1, NBEAL1, VPS13C, OSR1, SNX33, MITD1, MYLIP, NSMAF, ATG2B, SYTL4, MGLL, ASPSCR1, EPB41L4B, EPB41L1, EPB41L4A, DMBT1, BLOC1S6, SNX12, SNX6, EPB41L3, WDR45, WIPI2

GO:0019907

CC

cyclin-dependent protein kinase activating kinase holoenzyme complex

A cyclin-dependent kinase activating kinase complex capable of activating cyclin-dependent kinases by threonine phosphorylation, thus regulating cell cycle progression. consists of a kinase, cyclin and optional assembly factors, in human CDK7, CCNH and MNAT1. CAK activity is itself regulated throughout the cell cycle by T-loop phosphorylation of its kinase component (CDK7 in human). Phosphorylation of serine residues during mitosis inactivates the enzyme. Also capable of CAK phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II and other transcription activating proteins, as part of the general transcription factor TFIIH.

HSPD1, ERCC2, KDM5A, PUF60

GO:0019908

CC

nuclear cyclin-dependent protein kinase holoenzyme complex

Cyclin-dependent protein kinase (CDK) complex found in the nucleus.

CDK13, CDK12, BCCIP

GO:0020003

CC

symbiont-containing vacuole

Membrane-bounded vacuole within a host cell in which a symbiont organism resides. The vacuole membrane is derived from both the host and symbiont.

RAB29

GO:0020018

CC

ciliary pocket membrane

That part of the plasma membrane found in the ciliary pocket (also called flagellar pocket).

SNAP29, EHD3

GO:0022624

CC

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.

PSMD11, PSMD12, PSMD3, PSMC3, PSMC2, PSMC4, PSMC1, PSMC6, PSMD2

GO:0022625

CC

cytosolic large ribosomal subunit

The large subunit of a ribosome located in the cytosol.

RPLP1, RPLP2, RPLP0, RPL35A, RPL7, RPL17, RPL13, RPL10, RPL12, RPL22, RPL4, RPL13A, RPL35, RPL27A, RPL5, RPL21, RPL28, RPL29, RPL34, RPL14, RPL26, RPL15, RPL27, RPL37A, RPL37, RPL7A, RPL23A, RPL30, RPL31, RPL10A, RPL32, RPL11, RPL41, RPL38, RPL24, RPL36A, RPL19, RPL18A, RPL18, RPL22L1, RPL36AL, RPL39L, RPL36

GO:0022626

CC

cytosolic ribosome

A ribosome located in the cytosol.

APOD, RPL13, REPIN1, MRPL4, EIF2AK4, PPARGC1A, NUFIP1

GO:0022627

CC

cytosolic small ribosomal subunit

The small subunit of a ribosome located in the cytosol.

DDX3X, RPS17, RPSA, RPS2, RPS4Y1, RPS27, RPS9, RPS5, RPS10, RPS20, RPS3A, RPS7, RPS8, RPS15A, RPS16, RPS14, RPS18, RPS13, RPS11, RPS6, RPS25, RPS26, RPS27A, RPS21, HBA1, RPS27L, MRPS18A

GO:0030008

CC

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.

TRAPPC5, TRAPPC1

GO:0030014

CC

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.

CNOT1, CNOT3, CNOT4, ZFP36, CPEB3, CNOT7, CNOT6

GO:0030015

CC

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.

CNOT1, CNOT3

GO:0030016

CC

myofibril

The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.

CAPN3, TMOD1, LMOD1, ACTG1, MYBPC1, CALD1, TWF1, PDE4DIP, TWF2, MYH2, MYH4

GO:0030017

CC

sarcomere

The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.

MMP2, TPM1, TNNI3, TMOD1, LMOD1, CAPZB, CALM2, ACTC1, ARF1, ILK, ANKRD1, HABP4, MYH2, MYH4

GO:0030018

CC

Z disc

Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.

BIN1, FBP2, PPP1R12A, ACTN4, PPP1R12B, LDB3, OBSL1, DNAJB6, FLNB, NEBL, SORBS2, BMP10, CRYAB, HSPB1, KRT8, KRT19, DMD, ACTN1, JUP, DES, CAPN3, ATP2B4, MYL9, SRI, CTNNB1, ADRA1A, ACTN2, PSEN2, HDAC4, ANK2, DST, PPP3CA, NEXN, ANK3, CACNA1C, FLNC, PPP2R5A, RYR3, HOMER1, FBXO22, PALLD, SYNE2, TTN, RYR2, FBXO32, SYNC, MYOZ1, PARVA, MYOT, SYNPO2, STUB1

GO:0030027

CC

lamellipodium

A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.

MYO1G, HAX1, APBB1, WASL, ABLIM1, ITGB1BP1, ARPC3, CTNND1, FLOT1, PLEKHG5, SORBS2, ABLIM3, ITGB1, RAC2, CDH2, KITLG, NME2, APC, CTNNA2, DPP4, PTPRM, CORO1A, STX2, CTNNA1, CTNNB1, NF2, RDX, PIK3CA, VAMP7, RAC3, ACTR3, RHOA, ACTA2, RAC1, ACTG2, ACTC1, CDK5, PTK2, STX4, STX3, ILK, PKD2, DGKZ, IQGAP2, SNX1, DAG1, ARHGEF7, DPYSL3, CTTN, NEDD9, FAT1, SLC39A14, MYLK, ITSN1, PKN2, FSCN1, PTPRO, ARHGAP31, CCDC88A, AMOT, LRRC16A, TWF2, NHS, FGD6, RAPH1, RUFY3, CYFIP1, FGD2, ARPIN, PDPN, PLEKHH2, AMOTL1, PHACTR4, SCYL3, ABI1, ENAH, ARAP3, PALLD, APBB2, AJUBA, FGD4, SPATA13, ALS2, RAB3IP, CIB1, CORO1B, SH3BGRL3, TRPV4, MYO10, ABI2, EVL, CORO1C, PLXND1, WASF2

GO:0030054

CC

cell junction

A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.

SH3PXD2B, KCNK1, FBP2, DLGAP1, TOR1A, RGS12, FYB, SCAMP1, MUSK, SYNGR3, LZTS3, SRPX2, GABBR2, CLSTN1, UNC5C, SNAPIN, ADA, CHRM2, C4A, C4B, FBXO45, CHRNB1, BCR, ITGB4, PECAM1, SYN1, GAP43, CHRM3, SYT1, OSBP, CBLN1, MPST, CHRNA5, GABRA5, CDH5, CTNNA1, CTNNB1, GTF2F1, CHRNA7, SNCA, HTR2B, NAMPT, MAP1B, GRIA4, GLRB, NRIP1, PSEN1, PLXNA3, VAMP7, GTF2A2, ATN1, EPHA4, CTBP2, SNAP25, CXCR4, RHOA, NCS1, RAP1A, VAMP2, CXADR, DLG4, CDK5, CDK16, ICA1, FMR1, TJP1, KCNA1, SMAGP, ARHGEF5, GRIN2A, EPS8, DLG1, ILK, SNTA1, XRCC4, SSPN, ITSN1, VAMP3, RAB11B, PKN2, OCLN, C11orf73, SDK2, STXBP5, ARHGAP21, FAAP20, SARM1, CBLN3, NSMF, DSTYK, DNMBP, RUFY3, SV2B, ARC, RASGRP2, SDK1, CAMK2N1, LRRTM4, HOMER1, DCP2, ZDHHC17, SMC5, AMOTL1, NLGN4X, NLGN1, MINK1, ENAH, ATAD1, TRPV1, TMEM163, DMXL2, UTP15, DENND1A, PARD3, PPP1R13L, CACNG8, SYN2, KCTD12, CYFIP2, PERP, C8orf37, MAGI1, NEU1, GPER1, PKP4, P2RX4, SIGMAR1, OLFM1, PRRT1, PKP2, TMEM47, FERMT1, SYT11, PACSIN1, CDHR2, TRIM9, MFF, RIMS4, GOPC, PARD6A, NRN1, GPHN, DUOX2, HOMER3, CBLN4, DCAF13, GID8, DACT1, PSD3, CRIPT, GABBR1, BIN2, TJP2, TES, PUF60, NRXN1, SAMD4A, IGSF9B, RIMS2, COLQ, LZTS1, FARP1, DTNA, F11R, MRPS18B, ARFGEF2, PCLO

GO:0030055

CC

cell-substrate junction

A cell junction that forms a connection between a cell and the extracellular matrix.

DMD

GO:0030056

CC

hemidesmosome

A cell-substrate junction (attachment structure) found in epithelial cells that links intermediate filaments to extracellular matrices via transmembrane complexes. In vertebrates, hemidesmosomes mediate contact between the basal side of epithelial cells and the basal lamina. In C. elegans, hemidesmosomes connect epithelial cells to distinct extracellular matrices on both the apical and basal cell surfaces.

ITGB4, ITGA6, DST, COL17A1

GO:0030057

CC

desmosome

A cell-cell junction in which: on the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular anchor proteins; a bundle of keratin intermediate filaments is attached to the surface of each plaque; transmembrane adhesion proteins of the cadherin family bind to the plaques and interact through their extracellular domains to hold the adjacent membranes together by a Ca2+-dependent mechanism.

PPL, JUP, B4GALT1, DSP, UBA1, DSC2, DSG2, KAZN, PERP, PKP4, PKP2, JAM3, PNN, PKP3

GO:0030061

CC

mitochondrial crista

Any of the inward folds of the mitochondrial inner membrane. Their number, extent, and shape differ in mitochondria from different tissues and organisms. They appear to be devices for increasing the surface area of the mitochondrial inner membrane, where the enzymes of electron transport and oxidative phosphorylation are found. Their shape can vary with the respiratory state of the mitochondria.

OPA1, LYN, HSPD1, STAR

GO:0030112

CC

glycocalyx

A viscous, carbohydrate rich layer at the outermost periphery of a cell.

B4GALT1

GO:0030117

CC

membrane coat

Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules.

SYNJ1, CHMP2A, CHMP4B

GO:0030118

CC

clathrin coat

A membrane coat found on coated pits and some coated vesicles; consists of polymerized clathrin triskelions, each comprising three clathrin heavy chains and three clathrin light chains, linked to the membrane via one of the AP adaptor complexes.

CLTA, IGF2R

GO:0030119

CC

AP-type membrane coat adaptor complex

Any of several heterotetrameric complexes that link clathrin (or another coat-forming molecule, as hypothesized for AP-3 and AP-4) to a membrane surface; they are found on coated pits and coated vesicles, and mediate sorting of cargo proteins into vesicles. Each AP complex contains two large (a beta and one of either an alpha, gamma, delta, or epsilon) subunits (110-130 kDa), a medium (mu) subunit (approximately 50 kDa), and a small (sigma) subunit (15-20 kDa).

AP5Z1, AP3M2, AP1S2, AP5M1

GO:0030120

CC

vesicle coat

A membrane coat found on a coated vesicle.

SEC31A

GO:0030121

CC

AP-1 adaptor complex

A heterotetrameric AP-type membrane coat adaptor complex that consists of beta1, gamma, mu1 and sigma1 subunits and links clathrin to the membrane surface of a vesicle; vesicles with AP-1-containing coats are normally found primarily in the trans-Golgi network. In at least humans, the AP-1 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (gamma1 and gamma2, mu1A and mu1B, and sigma1A, sigma1B and sigma1C).

AP1G2, AP1S1, LDLRAP1, AFTPH, SYNRG

GO:0030122

CC

AP-2 adaptor complex

A heterotetrameric AP-type membrane coat adaptor complex that consists of alpha, beta2, mu2 and sigma2 subunits, and links clathrin to the membrane surface of a vesicle, and the cargo receptors during receptor/clathrin mediated endocytosis. Vesicles with AP-2-containing coats are normally found primarily near the plasma membrane, on endocytic vesicles. In at least humans, the AP-2 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different alpha genes (alphaA and alphaC).

AP2A2, EGFR, EPS15, AP2S1, AP2B1, PICALM, LDLRAP1, TBC1D5, AP2M1

GO:0030123

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AP-3 adaptor complex

A heterotetrameric AP-type membrane coat adaptor complex that consists of beta3, delta, mu3 and sigma3 subunits and is found associated with endosomal membranes. AP-3 does not appear to associate with clathrin in all organisms. In at least humans, the AP-3 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (beta3A and beta3B, mu3A and mu3B, and sigma3A and sigma3B).

AP3D1, AP3S2

GO:0030125

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clathrin vesicle coat

A clathrin coat found on a vesicle.

CLTA

GO:0030126

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COPI vesicle coat

One of two multimeric complexes that forms a membrane vesicle coat. The mammalian COPI subunits are called alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. Vesicles with COPI coats are found associated with Golgi membranes at steady state.

COPE, ARCN1, COPA, COPZ1, SCYL1, TMED3, COPG1

GO:0030127

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COPII vesicle coat

One of two multimeric complexes that forms a membrane vesicle coat. COPII is best characterized in S. cerevisiae, where the subunits are called Sar1p, Sec13p, Sec31p, Sec23p, and Sec24p. Vesicles with COPII coats are found associated with endoplasmic reticulum (ER) membranes at steady state.

SEC24D, SEC31A, SEC23A

GO:0030130

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clathrin coat of trans-Golgi network vesicle

A clathrin coat found on a vesicle of the trans-Golgi network.

CLTA, NCALD

GO:0030131

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clathrin adaptor complex

A membrane coat adaptor complex that links clathrin to a membrane.

AP3M2, AP1B1, GGA2, GGA1, AP3M1

GO:0030132

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clathrin coat of coated pit

The coat found on coated pits and the coated vesicles derived from coated pits; comprises clathrin and the AP-2 adaptor complex.

SYNJ1, CLTA, PICALM

GO:0030133

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transport vesicle

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

GOLIM4, COPE, SCAMP2, SURF4, KDELR3, VAMP4, SEC22B, AP1G2, IL33, INS, CD55, IGF2R, PRG2, BGN, KDELR1, PCSK1, ERP29, NTS, ARCN1, TMED10, RAB9A, CAV2, COPA, COPZ1, RAB11A, TMEM187, SSPN, TMED2, TRIP11, VAMP3, CNST, BLOC1S3, RABEPK, GALNT15, MYRIP, APH1B, ANKRD27, CHP1, SPX, CRISPLD2, RAB1B, TMEM168, PLEKHF2, ATP13A2, C14orf1, BLOC1S6, TMED3, COPG1

GO:0030134

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ER to Golgi transport vesicle

A vesicle that mediates transport from the endoplasmic reticulum to the Golgi complex; bears a coat formed of the COPII coat complex proteins; such vesicles found associated with endoplasmic reticulum (ER) membranes at steady state, and are involved in ER to Golgi (anterograde) vesicle transport.

SEC31A, F8, SERPINA1, APP, F5, CTSC, GOLGA2, KLHL12, TEX261, PCSK9, YIPF5, YIPF6, LMAN2L, CTSZ, IER3IP1

GO:0030135

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coated vesicle

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

HSPD1

GO:0030136

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clathrin-coated vesicle

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

HIP1, PIK3C2A, SCAMP1, STX6, SNX3, SLC2A4, FOLR1, NUMB, BCAP31, VAMP2, DAB2, OCRL, TNK2, FCHO2, MALL, VAMP3, AAK1, WIPI1, DENND1A, SNX18, SH3BP4, GGA2, SNX9

GO:0030137

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COPI-coated vesicle

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

TMED10, ARF1, TMED2, CCDC115, PACSIN1

GO:0030139

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endocytic vesicle

A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.

GOLIM4, STX7, MTSS1, PLEKHG5, ABCA1, APOA1, TF, RALA, IGF2R, CCL2, DRD2, RAB5A, DPP4, RAB5C, TIRAP, RAB5B, LRP2, HYAL2, PLD1, RABEP1, ITSN1, OCLN, AMOT, RAPGEF6, EHD3, MYO6

GO:0030140

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trans-Golgi network transport vesicle

A vesicle that mediates transport between the trans-Golgi network and other parts of the cell.

RAB27B, FURIN, IGF2R, SLC2A4, TMED10, GOPC

GO:0030141

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secretory granule

A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

RAB27B, EBAG9, TOR1A, SNAPIN, PLAT, POMC, IL1B, COL1A1, CHGB, MPO, SCG5, THBS1, HSPD1, PLA2G2A, VEGFA, CPE, RAB3B, TRH, ZP3, GAL, RAB27A, BRCA2, CLCN3, VAMP7, ZP1, CDC42, VAMP2, VAMP3, CARTPT, STXBP5, SLC30A8, PCSK5, SYTL4, STXBP5L, HILPDA

GO:0030173

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integral component of Golgi membrane

The component of the Golgi membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

B4GAT1, LARGE, ST6GAL1, ST8SIA6, GALNT2, ST3GAL1, ST3GAL3, ST3GAL4, ST3GAL2, TEX261, QSOX2, SGMS1, SGMS2, CSGALNACT1, ST8SIA4, MAN1C1, ST6GALNAC2, ST3GAL6, IER3IP1

GO:0030175

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filopodium

Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.

MYO1G, DNALI1, ITGB1, DMD, LCP1, B4GALT1, ACPP, EZR, VCAM1, KITLG, ITGA6, RDX, ACTN2, EPHA4, CDC42, ACTA2, ACTG2, ACTC1, CXADR, CDK5, TWF1, MTM1, IQGAP2, DAG1, DYNC1H1, FAT1, FSCN1, TWF2, RAPH1, RUFY3, PDPN, CD302, ABI1, ENAH, NGDN, FGF13, FGD4, SPATA13, DEF6, TRPV4, ABI2, FARP1, FAM65B

GO:0030176

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integral component of endoplasmic reticulum membrane

The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

ELOVL7, HACD1, UBXN8, SLC27A2, SLC37A4, ERN1, TM7SF2, HSPA5, ATF6, G6PC, SEC61A1, CLN3, ARL6IP1, EXT1, PIGG, HACD4, TEX261, HACD2, SYVN1, SGMS1, ANKLE2, XXYLT1, SGMS2, RHBDD1, EDEM1, PIGK, PIGT, DGAT2, DHRS9, VIMP, ESYT1, G6PC3, ELOVL1, DERL2, ELOVL4, PIGU, ELOVL6, RTN4, ELOVL5, HACD3, RRBP1, DPM3, DHCR7, AMFR, TMCO1, RCE1, TBL2

GO:0030285

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integral component of synaptic vesicle membrane

The component of the synaptic vesicle membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

ATP6V1G2, SYPL2, TMEM163

GO:0030286

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dynein complex

Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity.

DNAL4, DNAH14, DCTN2, DCTN1, DNAH12, DNAH10, DNAH11, DNAH9, DNAH1, HDAC6

GO:0030289

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protein phosphatase 4 complex

A protein serine/threonine phosphatase complex formed by the catalytic subunit of protein phosphatase 4 plus one or more regulatory subunits.

PPP4C

GO:0030315

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T-tubule

Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.

BIN1, SLC2A4, EZR, CAPN3, ATP2B4, SRI, RDX, ADRA1A, ATP1A2, ANK2, AHNAK, ANK3, AKAP6, CAMK2D, KCNJ11, STAC, SLC30A1

GO:0030424

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axon

The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.

BIN1, NRP1, SYNJ2, NCAM2, ADCY9, COBL, ZPR1, TNFRSF21, MYO1D, CA2, CST3, TGFB1, CRYAB, NTRK1, APP, CYP17A1, CCK, MME, C4A, C4B, MAPT, NEFH, ANXA3, DRD2, CREB1, GAP43, RAB5A, CNR1, COMT, MT3, CTNNA2, CANX, MAPK1, EPHB2, SLC6A1, CORO1A, SNCA, HTT, IQGAP1, PSEN1, PPT1, FXR1, NEK3, EPHA5, EPHB1, EPHA4, PRSS12, MTPN, TGFB2, NCS1, YWHAE, RAB11A, IRX3, CDK5, DST, FMR1, TUBB3, MTMR2, ALCAM, SEMA3A, GRM3, NECTIN1, PTPRK, PTPRO, LDLRAP1, SARM1, KLHL24, RUFY3, SETX, HOMER1, CNTN4, MINK1, TMEM57, NGDN, UHMK1, PALLD, FGF13, ROBO3, DOCK7, ALS2, KIF20B, GPER1, FEZ1, OLFM1, CIB1, SYT11, KATNB1, PINK1, SEMA6A, ADGRL3, KIF13B, STMN3, TENM3, HDAC6, GHRL, ADAM21, DICER1, RNF6, DTNA

GO:0030425

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dendrite

A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.

KCNK1, CHL1, RGS12, GRM6, HNRNPR, OPA1, BRINP1, ADCY9, COBL, SRSF10, URI1, ZWINT, STAU1, GNRH1, PENK, APOE, BGLAP, NTRK1, CYBB, GNAI2, APOD, RPLP0, CCK, TH, CHRM2, MME, C4A, C4B, MAPT, LAMP1, ANXA3, CCL2, DRD2, IFNGR1, GNB3, SYN1, ELK1, CHRM3, RAB5A, NR1D1, HTR2C, EPHB2, GABRA5, HTR7, BMPR1A, IL6ST, HTR2B, HTT, SLC1A4, RANGAP1, RPL28, GRIA4, GLRB, GNAQ, PPT1, RAB27A, KPNA1, EPHA5, EPHB1, EPHA4, PRSS12, NCS1, RPS6, GNB1, RACK1, GNAS, RBM3, CDK5, PURA, NRG1, FMR1, KCNA1, ANK3, BNIP3, STRN3, STX3, TUBB3, MTMR2, ALCAM, BMPR2, CAPRIN1, SEMA3A, PTPRK, DPYSL2, DBN1, CPEB4, GNAS, CPLX2, SARM1, NSMF, KNDC1, RUFY3, CAMK2N1, MAGI2, NLGN4X, NLGN1, MINK1, CPEB3, NGDN, TRPV1, TMEM185A, DNER, DENND1A, SLC9A6, FGF13, ERO1A, ALS2, GPER1, FEZ1, TXN2, CIB1, MLPH, TRIM9, MAGEE1, GOPC, GPHN, GLRX2, ELOVL5, PLK2, CRIPT, ATXN10, HDAC6, GABBR1, LAMP5, AMFR, AGO2, TAOK2, MAPK8IP3, SAMD4A, IGSF9B, DICER1, FARP1, RBM8A

GO:0030426

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growth cone

The migrating motile tip of a growing nerve cell axon or dendrite.

APBB1, TOR1A, NRP1, ARPC3, HNRNPR, CTNND1, ZPR1, ANG, MAPT, TIMP2, CNR1, ITGA3, OTX2, SNCA, IQGAP1, CSNK1E, PSEN1, GSK3B, RAC3, SNAP25, CALM2, CXADR, CDK5, FMR1, EPS8, STX3, DCTN2, DPYSL3, CTTN, DPYSL2, DBN1, FSCN1, PTPRO, TWF2, RUFY3, SETX, SIRT2, ABI1, PALLD, APBB2, FGF13, DOCK7, ALS2, KIF20B, ORAI2, SIGMAR1, CIB1, KATNB1, TRPV4, PCDH9, CRTAC1, STMN3, PTBP2, AMFR, NDRG2, DICER1, MYO5A

GO:0030427

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site of polarized growth

Any part of a cell where non-isotropic growth takes place.

FRY

GO:0030478

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actin cap

Polarized accumulation of cytoskeletal proteins (including F-actin) and regulatory proteins in a cell. An example of this is the actin cap found in Saccharomyces cerevisiae.

WASL, ACTR2, CALD1

GO:0030485

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smooth muscle contractile fiber

The contractile fiber of smooth muscle cells.

ACTA2

GO:0030496

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midbody

A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.

AURKA, BIRC5, PRC1, CTNND1, RAB11FIP3, TACC1, RNF8, KIF20A, KIF4A, GNAI2, CDK1, ANXA2, GNAI3, RAP2A, HSPA5, SLC2A1, RALA, RALB, HSP90B1, MAK, GDI1, RDX, PPP1CC, IQGAP1, CENPF, ANXA11, NEK2, PLK1, IST1, GEM, CDC42, RHOA, GNAI1, RACK1, ERH, CENPE, KIF23, PTCH1, SEPT6, FAM175B, SEPT2, KIF14, SEPT7, PKN1, PKN2, CEP55, CDCA8, TTC19, PSRC1, C6orf89, TEX14, SIRT2, ASPM, SPG20, PIK3C3, SHCBP1, FLCN, MPLKIP, MITD1, ARL8A, AURKB, ZFYVE19, KIF20B, SPAG5, PKP4, KATNB1, CEP44, RACGAP1, TRIOBP, CHMP4B, ECT2, CYLD, ARL8B, KLHL9, KLHL13, SPAST, MAPRE3, SH3GLB1, ZNF330

GO:0030529

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intracellular ribonucleoprotein complex

An intracellular macromolecular complex containing both protein and RNA molecules.

XPO1, HNRNPR, ACTN4, SYNCRIP, GAPDH, RPLP0, SSB, NPM1, EPRS, HNRNPA1, TROVE2, EEF2, HNRNPL, DDX5, RPL7, HNRNPA2B1, ZFP36, RPL22, RPL4, NUP62, RBMX, BRCA1, RPL13A, LRPPRC, RPL5, RPS9, RPS5, CSNK1A1, CSNK1E, GSK3B, HNRNPA3, HNRNPH2, PCBP4, ACTB, RPS3A, RPL27, RPS7, RPS8, RPS6, YBX1, HNRNPU, FMR1, ZFP36L1, NCBP1, ILF2, ILF3, G3BP1, NFATC2, HNRNPD, BOP1, SLBP, PCBP1, LARP7, JMJD6, PABPN1, MRPL41, DYRK2, SECISBP2L, TEFM, SECISBP2, HNRNPAB, TEP1, LARP6, HNRNPUL1, SLIRP, APOBEC3G, SRA1, PUF60, AGO2, G3BP2, PA2G4

GO:0030532

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small nuclear ribonucleoprotein complex

A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs.

SNRPA1, SNRPB, GEMIN4, SNRPF, LSM6, SNRPD1, SNRPD2, SNRPD3, SNRPN

GO:0030658

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transport vesicle membrane

The lipid bilayer surrounding a transport vesicle.

HLA-DRA, HLA-DQA2, HLA-DQA1, HLA-DQB1, CD74, HLA-DRB4, CPE, HLA-DPA1, CA4, AQP2, CLCN3, VAMP7, HLA-DRB3, SNTB2, HLA-DRB5, ARFGEF3, SLC30A8, SYTL4, TMEM30A, RPH3AL

GO:0030659

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cytoplasmic vesicle membrane

The lipid bilayer surrounding a cytoplasmic vesicle.

TOR1A, PDE6D, KIF1B, TBC1D4, FZD6, ANXA1, RALA, SLC2A4, CLIP1, YWHAB, SFN, IFNGR2, HTT, RNF144A, AP3M2, AP1S2, AP3S2, AP1S1, YWHAE, RAB11A, YWHAZ, YWHAH, TNK2, SMAGP, AP1B1, MARCH8, STXBP5, ARHGAP21, DENND4C, AGTRAP, LRIG3, RAB11FIP2, C2CD5, ZDHHC17, GPRC5A, MARCH1, SNX33, SNX19, APPBP2, SNX21, ANKRD27, SNX18, GPER1, PACSIN1, GABARAPL1, RHBG, GPRC5C, SNX15, FMN2, GDE1, GPRC5B, FLRT1, LNPEP, LAMP5, RAB21, TAOK2, MYO5B, AP3M1, SNX24, SNX9, SNX5

GO:0030660

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Golgi-associated vesicle membrane

The lipid bilayer surrounding a vesicle associated with the Golgi apparatus.

GPR89A, CSPG5, GPR89B, CFTR, RHOQ, GJA1, PKD1, ZDHHC17, SPPL3, SPPL2A, HM13, GOPC, ITM2B

GO:0030663

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COPI-coated vesicle membrane

The lipid bilayer surrounding a COPI-coated vesicle.

KDELR1, TMED2

GO:0030665

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clathrin-coated vesicle membrane

The lipid bilayer surrounding a clathrin-coated vesicle.

HIP1, DAB2, VAMP3, DENND1A, CEMIP, MYO6

GO:0030666

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endocytic vesicle membrane

The lipid bilayer surrounding an endocytic vesicle.

WASL, AP2A2, HLA-DRA, HLA-DQA2, HLA-DQA1, HLA-DQB1, CD74, UBC, HLA-DRB4, CD36, HLA-DPA1, CD9, NOS3, WNT5A, GRIA4, AP2S1, WNT3, RPS27A, UBA52, AP2B1, DLG4, HLA-DRB3, MDM2, CAV1, CAMK2D, PTCH1, SCARF1, HLA-DRB5, COLEC12, WLS, CD163, NOSTRIN, SCARB1, STAB2, CACNG8, AP2M1, HBEGF, WNT5B, STAB1, WNT6

GO:0030667

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secretory granule membrane

The lipid bilayer surrounding a secretory granule.

EXOC3, CPE, PAM, CA4, TMED10, RAB27A, VAMP7, VAMP2, ICA1, ITPR2, ITPR3, SLC30A8, RPH3AL

GO:0030669

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clathrin-coated endocytic vesicle membrane

The lipid bilayer surrounding a clathrin-coated endocytic vesicle.

AP2A2, LDLR, HLA-DRA, HLA-DQA2, HLA-DQA1, HLA-DQB1, APOB, CD74, FCGR1A, HLA-DRB4, HLA-DPA1, CD9, WNT5A, AP2S1, AP1S2, AP1S1, AP2B1, HLA-DRB3, AP1B1, HLA-DRB5, FCGR1B, AP2M1, HBEGF, SH3GL2, FZD4