5NZS

The structure of the COPI coat leaf in complex with the ArfGAP2 uncoating factor


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
DSCOP2B SuperfamilySNARE-like8082715 3001113 SCOP2B (2022-06-29)
E [auth F]SCOP2B SuperfamilyRas-like P-loop GTPases8089854 3002022 SCOP2B (2022-06-29)
G [auth R]SCOP2B SuperfamilyRas-like P-loop GTPases8089854 3002022 SCOP2B (2022-06-29)
K [auth M]SCOP2B SuperfamilyRas-like P-loop GTPases8089854 3002022 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF00400e5nzsA1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
APF04053e5nzsA3 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF04053ECOD (1.6)
APF04053e5nzsA2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: PF04053ECOD (1.6)
BPF07718e5nzsB3 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07718ECOD (1.6)
BPF01602e5nzsB2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: PF01602ECOD (1.6)
BPF14806e5nzsB1 A: a+b two layersX: TBP-likeH: Subdomain of clathrin and coatomer appendage domain (From Topology)T: Subdomain of clathrin and coatomer appendage domainF: PF14806ECOD (1.6)
E [auth F]PF00025e5nzsF1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF00025ECOD (1.6)
G [auth R]PF00025e5nzsR1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF00025ECOD (1.6)
K [auth M]PF00025e5nzsM1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF00025ECOD (1.6)
F [auth G]PF08752e5nzsG1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF08752ECOD (1.6)
F [auth G]PF01602e5nzsG2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: PF01602ECOD (1.6)
F [auth G]PF16381e5nzsG3 A: a+b two layersX: TBP-likeH: Subdomain of clathrin and coatomer appendage domain (From Topology)T: Subdomain of clathrin and coatomer appendage domainF: PF16381ECOD (1.6)
I [auth K]PF08752e5nzsK2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF08752ECOD (1.6)
I [auth K]PF01602e5nzsK1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: PF01602ECOD (1.6)
I [auth K]PF16381e5nzsK3 A: a+b two layersX: TBP-likeH: Subdomain of clathrin and coatomer appendage domain (From Topology)T: Subdomain of clathrin and coatomer appendage domainF: PF16381ECOD (1.6)
H [auth Z]PF01217e5nzsZ1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: PF01217ECOD (1.6)
J [auth L]PF01217e5nzsL1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: PF01217ECOD (1.6)
L [auth P]PF01412e5nzsP1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: PF01412ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF04053Coatomer WD associated region (Coatomer_WDAD)Coatomer WD associated region- Repeat
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
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
PF04053Coatomer WD associated region (Coatomer_WDAD)Coatomer WD associated region- Repeat
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chain- Domain
E [auth F],
G [auth R],
K [auth M]
PF00025ADP-ribosylation factor family (Arf)ADP-ribosylation factor familyPfam combines a number of different Prosite families togetherDomain
F [auth G],
I [auth K]
PF01602Adaptin N terminal region (Adaptin_N)Adaptin N terminal region- Repeat
F [auth G],
I [auth K]
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
F [auth G],
I [auth K]
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
H [auth Z],
J [auth L]
PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chain- Domain
L [auth P]PF01412Putative GTPase activating protein for Arf (ArfGap)Putative GTPase activating protein for ArfPutative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Coatomer subunit alpha
Coatomer subunit beta
Coatomer subunit beta'
Coatomer subunit delta-
E [auth F],
G [auth R],
K [auth M]
ADP-ribosylation factor 1
F [auth G],
I [auth K]
Coatomer subunit gamma-1
H [auth Z],
J [auth L]
Coatomer subunit zeta-1-
L [auth P]ADP-ribosylation factor GTPase-activating protein 2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR019775WD40 repeat, conserved siteConserved Site
IPR016391Coatomer subunit alphaFamily
IPR010714Coatomer, alpha subunit, C-terminalDomain
IPR047312Coatomer subunit alpha, WD Associated RegionDomain
IPR011048Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamilyHomologous Superfamily
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
IPR006692Coatomer, WD associated regionDomain
IPR001680WD40 repeatRepeat
IPR020472G-protein beta WD-40 repeatRepeat
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
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
IPR016453Coatomer beta' subunit (COPB2)Family
IPR006692Coatomer, WD associated regionDomain
IPR001680WD40 repeatRepeat
IPR020472G-protein beta WD-40 repeatRepeat
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
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
E [auth F],
G [auth R],
K [auth M]
IPR045872ADP-ribosylation factor 1-5Family
E [auth F],
G [auth R],
K [auth M]
IPR005225Small GTP-binding protein domainDomain
E [auth F],
G [auth R],
K [auth M]
IPR006689Small GTPase superfamily, ARF/SAR typeFamily
E [auth F],
G [auth R],
K [auth M]
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
F [auth G],
I [auth K]
IPR016024Armadillo-type foldHomologous Superfamily
F [auth G],
I [auth K]
IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
F [auth G],
I [auth K]
IPR013040Coatomer, gamma subunit, appendage, Ig-like subdomainDomain
F [auth G],
I [auth K]
IPR013041Clathrin adaptor, appendage, Ig-like subdomain superfamilyHomologous Superfamily
F [auth G],
I [auth K]
IPR011989Armadillo-like helicalHomologous Superfamily
F [auth G],
I [auth K]
IPR032154Coatomer subunit gamma, C-terminalDomain
F [auth G],
I [auth K]
IPR017106Coatomer gamma subunitFamily
F [auth G],
I [auth K]
IPR037067Coatomer, gamma subunit, appendage domain superfamilyHomologous Superfamily
F [auth G],
I [auth K]
IPR012295TBP domain superfamilyHomologous Superfamily
F [auth G],
I [auth K]
IPR009028Coatomer/calthrin adaptor appendage, C-terminal subdomainHomologous Superfamily
H [auth Z],
J [auth L]
IPR000804Clathrin adaptor complex, small chainConserved Site
H [auth Z],
J [auth L]
IPR022775AP complex, mu/sigma subunitDomain
H [auth Z],
J [auth L]
IPR039652Coatomer subunit zetaFamily
H [auth Z],
J [auth L]
IPR011012Longin-like domain superfamilyHomologous Superfamily
L [auth P]IPR037278ARFGAP/RecO-like zinc fingerHomologous Superfamily
L [auth P]IPR001164Arf GTPase activating proteinDomain
L [auth P]IPR038508ArfGAP domain superfamilyHomologous Superfamily