5A1U | pdb_00005a1u

The structure of the COPI coat triad


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
HSCOP2 FamilyClathrin coat assembly domain 8082714 4002754 SCOP2 (2022-06-29)
HSCOP2 SuperfamilySNARE-like 8082715 3001113 SCOP2 (2022-06-29)
BSCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
HPenicil_amidasee5a1uH1 A: a/b three-layered sandwichesX: Rossmann-likeH: 26S proteasome subunit Rpn2 C-terminal domainT: 26S proteasome subunit Rpn2 C-terminal domainF: Penicil_amidaseECOD (v294.1)
GCoatamer_beta_Ce5a1uG2 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: Coatamer_beta_CECOD (v294.1)
GRAI1e5a1uG3 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
GGlycos_transf_1e5a1uG1 A: a/b three-layered sandwichesX: omega toxin-likeH: omega toxin-relatedT: omega toxin-relatedF: Glycos_transf_1ECOD (v294.1)
FClat_adaptor_se5a1uF1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: Clat_adaptor_sECOD (v294.1)
EClat_adaptor_se5a1uE1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: Clat_adaptor_sECOD (v294.1)
EGlycos_transf_1e5a1uE3 A: a/b three-layered sandwichesX: omega toxin-likeH: omega toxin-relatedT: omega toxin-relatedF: Glycos_transf_1ECOD (v294.1)
DClat_adaptor_se5a1uD1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: Clat_adaptor_sECOD (v294.1)
CPhyHe5a1uC1 A: a/b three-layered sandwichesX: ssDNA-binding transcriptional regulator domain-likeH: ssDNA-binding transcriptional regulator domainT: ssDNA-binding transcriptional regulator domainF: PhyHECOD (v294.1)
BClat_adaptor_se5a1uB1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: Clat_adaptor_sECOD (v294.1)
AClat_adaptor_se5a1uA1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: Clat_adaptor_sECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
PF01602Adaptin N terminal region (Adaptin_N)Adaptin N terminal region- Repeat
PF14806Coatomer beta subunit appendage platform (Coatomer_b_Cpla)Coatomer beta subunit appendage platformThis family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). It is a platform domain on the appendage that carries a highly conserved tryptophan. Domain
PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
PF01602Adaptin N terminal region (Adaptin_N)Adaptin N terminal region- Repeat
PF16381Coatomer subunit gamma-1 C-terminal appendage platform (Coatomer_g_Cpla)Coatomer subunit gamma-1 C-terminal appendage platformCoatomer_g_Cpla is the very C-terminal domain of the eukaryotic Coatomer subunit gamma-1 proteins. It acts as a platform domain to the C-terminal appendage. It carries one single protein/protein interaction site, which is the binding site for ARFGAP2 ...Coatomer_g_Cpla is the very C-terminal domain of the eukaryotic Coatomer subunit gamma-1 proteins. It acts as a platform domain to the C-terminal appendage. It carries one single protein/protein interaction site, which is the binding site for ARFGAP2 or ADP-ribosylation factor GTPase-activating protein. COPI-coated vesicles mediate retrograde transport from the Golgi back to the ER and intra-Golgi transport. The gamma-COPI is part of one of two subcomplexes that make up the heptameric coatomer complex along with the beta, delta and zeta subunits [1].
Domain
PF08752Coatomer gamma subunit appendage platform subdomain (COP-gamma_platf)Coatomer gamma subunit appendage platform subdomainCOPI-coated vesicles function in retrograde transport from the Golgi to the ER, and in intra-Golgi transport. This is the platform subdomain of the coatomer gamma subunit appendage domain. It carries a protein-protein interaction site at U ...COPI-coated vesicles function in retrograde transport from the Golgi to the ER, and in intra-Golgi transport. This is the platform subdomain of the coatomer gamma subunit appendage domain. It carries a protein-protein interaction site at UniProt:P53620, residue W776, which in yeast binds to the ARFGAP Glo3p, and in mammalian gamma-COP binds to a Glo3p orthologue, ARFGAP2 [1].
Domain
PF04053COPA/B second beta-propeller (B-prop_COPA_B_2nd)COPA/B second beta-propeller- Repeat
PF23953COPA/B TPR domain (TPR_COPA_B)COPA/B TPR domain- Repeat
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF04053COPA/B second beta-propeller (B-prop_COPA_B_2nd)COPA/B second beta-propeller- Repeat
PF23953COPA/B TPR domain (TPR_COPA_B)COPA/B TPR domain- Repeat
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
COATOMER SUBUNIT DELTA-
COATOMER SUBUNIT BETA
COATOMER SUBUNIT ZETA-1-
COATOMER SUBUNIT GAMMA-1
COATOMER SUBUNIT BETA'
COATOMER SUBUNIT ALPHA
A, B
ADP-RIBOSYLATION FACTOR 1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR011012Longin-like domain superfamilyHomologous Superfamily
IPR027059Coatomer delta subunitFamily
IPR022775AP complex, mu/sigma subunitDomain
IPR036168AP-2 complex subunit mu, C-terminal superfamilyHomologous Superfamily
IPR028565Mu homology domainDomain
IPR016460Coatomer beta subunit (COPB1)Family
IPR016024Armadillo-type foldHomologous Superfamily
IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
IPR011710Coatomer beta subunit, C-terminalDomain
IPR029446Coatomer beta subunit, appendage platform domainDomain
IPR011989Armadillo-like helicalHomologous Superfamily
IPR000804Clathrin adaptor complex, small chainConserved Site
IPR022775AP complex, mu/sigma subunitDomain
IPR039652Coatomer subunit zetaFamily
IPR011012Longin-like domain superfamilyHomologous Superfamily
IPR016024Armadillo-type foldHomologous Superfamily
IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
IPR013040Coatomer, gamma subunit, appendage, Ig-like subdomainDomain
IPR013041Clathrin adaptor, appendage, Ig-like subdomain superfamilyHomologous Superfamily
IPR011989Armadillo-like helicalHomologous Superfamily
IPR032154Coatomer subunit gamma, C-terminalDomain
IPR017106Coatomer gamma subunitFamily
IPR037067Coatomer, gamma subunit, appendage domain superfamilyHomologous Superfamily
IPR012295TBP domain superfamilyHomologous Superfamily
IPR009028Coatomer/calthrin adaptor appendage, C-terminal subdomainHomologous Superfamily
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
IPR016453Coatomer beta' subunit (COPB2)Family
IPR050844Coatomer complex subunitFamily
IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
IPR001680WD40 repeatRepeat
IPR006692COPA/B, second beta-propeller domainDomain
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
IPR056176COPA/B, TPR domainDomain
IPR019775WD40 repeat, conserved siteConserved Site
IPR016391Coatomer subunit alphaFamily
IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
IPR010714Coatomer, alpha subunit, C-terminalDomain
IPR006692COPA/B, second beta-propeller domainDomain
IPR047312Coatomer subunit alpha, WD Associated RegionDomain
IPR011048Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamilyHomologous Superfamily
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
IPR056176COPA/B, TPR domainDomain
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
IPR050844Coatomer complex subunitFamily
IPR001680WD40 repeatRepeat
A, B
IPR005225Small GTP-binding domainDomain
A, B
IPR045872ADP-ribosylation factor 1-5Family
A, B
IPR024156Small GTPase superfamily, ARF typeFamily
A, B
IPR006689Small GTPase superfamily, ARF/SAR typeFamily
A, B
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily