5A1V | pdb_00005a1v

The structure of the COPI coat linkage I


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
HSCOP2B SuperfamilySNARE-like 8082715 3001113 SCOP2B (2022-06-29)
PSCOP2B SuperfamilySNARE-like 8082715 3001113 SCOP2B (2022-06-29)
YSCOP2B SuperfamilySNARE-like 8082715 3001113 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
SSCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
ISCOP2B 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)
Ze5a1vZ1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F:ECOD (v294.1)
QRAI1e5a1vQ1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
HPhyHe5a1vH1 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)
PPhyHe5a1vP1 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)
YPhyHe5a1vY1 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)
Oe5a1vO2 A: a/b three-layered sandwichesX: cradle loop barrelH: RIFT-relatedT: acid proteaseF:ECOD (v294.1)
Oe5a1vO4 A: a/b three-layered sandwichesX: omega toxin-likeH: omega toxin-relatedT: omega toxin-relatedF:ECOD (v294.1)
XGlyco_hydro_31_3rde5a1vX2 A: a/b three-layered sandwichesX: jelly-rollH: Acetamidase/Formamidase-likeT: Acetamidase/Formamidase-likeF: Glyco_hydro_31_3rdECOD (v294.1)
Xe5a1vX4 A: a/b three-layered sandwichesX: omega toxin-likeH: omega toxin-relatedT: omega toxin-relatedF:ECOD (v294.1)
Ge5a1vG2 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F:ECOD (v294.1)
Ge5a1vG1 A: a/b three-layered sandwichesX: omega toxin-likeH: omega toxin-relatedT: omega toxin-relatedF:ECOD (v294.1)
Fe5a1vF1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F:ECOD (v294.1)
Ne5a1vN1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F:ECOD (v294.1)
We5a1vW1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F:ECOD (v294.1)
Ee5a1vE1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F:ECOD (v294.1)
EGlycos_transf_1e5a1vE3 A: a/b three-layered sandwichesX: omega toxin-likeH: omega toxin-relatedT: omega toxin-relatedF: Glycos_transf_1ECOD (v294.1)
VGlyco_hydro_31_3rde5a1vV1 A: a/b three-layered sandwichesX: jelly-rollH: Acetamidase/Formamidase-likeT: Acetamidase/Formamidase-likeF: Glyco_hydro_31_3rdECOD (v294.1)
VGlycos_transf_1e5a1vV3 A: a/b three-layered sandwichesX: omega toxin-likeH: omega toxin-relatedT: omega toxin-relatedF: Glycos_transf_1ECOD (v294.1)
Me5a1vM1 A: a/b three-layered sandwichesX: cradle loop barrelH: RIFT-relatedT: acid proteaseF:ECOD (v294.1)
MGlycos_transf_1e5a1vM3 A: a/b three-layered sandwichesX: omega toxin-likeH: omega toxin-relatedT: omega toxin-relatedF: Glycos_transf_1ECOD (v294.1)
URAI1e5a1vU1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
LPhyHe5a1vL1 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)
DRAI1e5a1vD1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
TRAI1e5a1vT2 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
TGlutaredoxin, ArsCe5a1vT5 A: a/b three-layered sandwichesX: PriB N-terminal domain-likeH: Aconitase iron-sulfur domainT: Aconitase iron-sulfur domainF: Glutaredoxin, ArsCECOD (v294.1)
Ke5a1vK2 A: a/b three-layered sandwichesX: Lipocalins/StreptavidinH: Fibronectin type I module-likeT: Fibronectin type I moduleF:ECOD (v294.1)
KGlyco_hydro_66e5a1vK5 A: a/b three-layered sandwichesX: Lipocalins/StreptavidinH: SAM/DNA-glycosylaseT: SAM domain-likeF: Glyco_hydro_66ECOD (v294.1)
KRad60-SLDe5a1vK4 A: a/b three-layered sandwichesX: Phosphorylase/hydrolase-likeH: Ribosomal protein S5 domain 2-likeT: Ribosomal protein S5 domain 2-likeF: Rad60-SLDECOD (v294.1)
CPhyHe5a1vC1 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)
BRAI1e5a1vB1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
SRAI1e5a1vS1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
RRAI1e5a1vR1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
JRAI1e5a1vJ1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
IRAI1e5a1vI1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)
ARAI1e5a1vA1 A: a/b three-layered sandwichesX: Ribosomal protein S7H: Ribosomal protein S7T: Ribosomal protein S7F: RAI1ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
H, P, Y
PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
G, O, X
PF01602Adaptin N terminal region (Adaptin_N)Adaptin N terminal region- Repeat
G, O, X
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
F, N, W
PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
E, M, V
PF01602Adaptin N terminal region (Adaptin_N)Adaptin N terminal region- Repeat
E, M, V
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
E, M, V
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
D, L, U
PF04053COPA/B second beta-propeller (B-prop_COPA_B_2nd)COPA/B second beta-propeller- Repeat
D, L, U
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
D, L, U
PF23953COPA/B TPR domain (TPR_COPA_B)COPA/B TPR domain- Repeat
C, K, T
PF04053COPA/B second beta-propeller (B-prop_COPA_B_2nd)COPA/B second beta-propeller- Repeat
C, K, T
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
C, K, T
PF23953COPA/B TPR domain (TPR_COPA_B)COPA/B TPR domain- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Q, Z
COATOMER SUBUNIT EPSILON
H, P, Y
COATOMER SUBUNIT DELTA-
G, O, X
COATOMER SUBUNIT BETA'
F, N, W
COATOMER SUBUNIT ZETA-1-
E, M, V
COATOMER SUBUNIT GAMMA-1
D, L, U
COATOMER SUBUNIT BETA
C, K, T
COATOMER SUBUNIT ALPHA
A, B, I, J, R
ADP-RIBOSYLATION FACTOR 1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
Q, Z
IPR006822Coatomer, epsilon subunitFamily
Q, Z
IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
H, P, Y
IPR011012Longin-like domain superfamilyHomologous Superfamily
H, P, Y
IPR027059Coatomer delta subunitFamily
H, P, Y
IPR022775AP complex, mu/sigma subunitDomain
H, P, Y
IPR036168AP-2 complex subunit mu, C-terminal superfamilyHomologous Superfamily
H, P, Y
IPR028565Mu homology domainDomain
G, O, X
IPR016460Coatomer beta subunit (COPB1)Family
G, O, X
IPR016024Armadillo-type foldHomologous Superfamily
G, O, X
IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
G, O, X
IPR011710Coatomer beta subunit, C-terminalDomain
G, O, X
IPR029446Coatomer beta subunit, appendage platform domainDomain
G, O, X
IPR011989Armadillo-like helicalHomologous Superfamily
F, N, W
IPR000804Clathrin adaptor complex, small chainConserved Site
F, N, W
IPR022775AP complex, mu/sigma subunitDomain
F, N, W
IPR039652Coatomer subunit zetaFamily
F, N, W
IPR011012Longin-like domain superfamilyHomologous Superfamily
E, M, V
IPR016024Armadillo-type foldHomologous Superfamily
E, M, V
IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
E, M, V
IPR013040Coatomer, gamma subunit, appendage, Ig-like subdomainDomain
E, M, V
IPR013041Clathrin adaptor, appendage, Ig-like subdomain superfamilyHomologous Superfamily
E, M, V
IPR011989Armadillo-like helicalHomologous Superfamily
E, M, V
IPR032154Coatomer subunit gamma, C-terminalDomain
E, M, V
IPR017106Coatomer gamma subunitFamily
E, M, V
IPR037067Coatomer, gamma subunit, appendage domain superfamilyHomologous Superfamily
E, M, V
IPR012295TBP domain superfamilyHomologous Superfamily
E, M, V
IPR009028Coatomer/calthrin adaptor appendage, C-terminal subdomainHomologous Superfamily
D, L, U
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
D, L, U
IPR016453Coatomer beta' subunit (COPB2)Family
D, L, U
IPR050844Coatomer complex subunitFamily
D, L, U
IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
D, L, U
IPR001680WD40 repeatRepeat
D, L, U
IPR006692COPA/B, second beta-propeller domainDomain
D, L, U
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
D, L, U
IPR056176COPA/B, TPR domainDomain
C, K, T
IPR019775WD40 repeat, conserved siteConserved Site
C, K, T
IPR016391Coatomer subunit alphaFamily
C, K, T
IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
C, K, T
IPR010714Coatomer, alpha subunit, C-terminalDomain
C, K, T
IPR006692COPA/B, second beta-propeller domainDomain
C, K, T
IPR047312Coatomer subunit alpha, WD Associated RegionDomain
C, K, T
IPR011048Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamilyHomologous Superfamily
C, K, T
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
C, K, T
IPR056176COPA/B, TPR domainDomain
C, K, T
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
C, K, T
IPR050844Coatomer complex subunitFamily
C, K, T
IPR001680WD40 repeatRepeat
A, B, I, J, R
IPR005225Small GTP-binding domainDomain
A, B, I, J, R
IPR045872ADP-ribosylation factor 1-5Family
A, B, I, J, R
IPR024156Small GTPase superfamily, ARF typeFamily
A, B, I, J, R
IPR006689Small GTPase superfamily, ARF/SAR typeFamily
A, B, I, J, R
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily