5NZV | pdb_00005nzv

The structure of the COPI coat linkage IV

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
FSCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
L [auth M]SCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
V [auth T]SCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
R [auth P]SCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
H [auth R]SCOP2B SuperfamilyRas-like P-loop GTPases 8089854 3002022 SCOP2B (2022-06-29)
E [auth D]SCOP2B SuperfamilySNARE-like 8082715 3001113 SCOP2B (2022-06-29)
Q [auth N]SCOP2B SuperfamilySNARE-like 8082715 3001113 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
M [auth H]ECH_1e5nzvH1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
M [auth H]Glutaredoxin, ArsCe5nzvH5 A: a/b three-layered sandwichesX: PriB N-terminal domain-likeH: Aconitase iron-sulfur domainT: Aconitase iron-sulfur domainF: Glutaredoxin, ArsCECOD (v294.1)
AECH_1e5nzvA2 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
AGlutaredoxin, ArsCe5nzvA5 A: a/b three-layered sandwichesX: PriB N-terminal domain-likeH: Aconitase iron-sulfur domainT: Aconitase iron-sulfur domainF: Glutaredoxin, ArsCECOD (v294.1)
B [auth E]ECH_1e5nzvE1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
N [auth O]ECH_1e5nzvO1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
C [auth B]ECH_1e5nzvB1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
O [auth I]ECH_1e5nzvI1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
GECH_1e5nzvG1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
J [auth K]ECH_1e5nzvK1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
T [auth Q]ECH_1e5nzvQ1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
I [auth Z]ECH_1e5nzvZ1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
U [auth S]ECH_1e5nzvS1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
S [auth U]ECH_1e5nzvU1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
K [auth L]ECH_1e5nzvL1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
FECH_1e5nzvF1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
L [auth M]ECH_1e5nzvM1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
V [auth T]ECH_1e5nzvT1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
R [auth P]ECH_1e5nzvP1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)
H [auth R]ECH_1e5nzvR1 A: a/b three-layered sandwichesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A,
M [auth H]		PF04053COPA/B second beta-propeller (B-prop_COPA_B_2nd)COPA/B second beta-propeller- Repeat
A,
M [auth H]		PF23953COPA/B TPR domain (TPR_COPA_B)COPA/B TPR domain- Repeat
A,
M [auth H]		PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
C [auth B],
O [auth I]		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
D [auth C],
P [auth J]		PF04053COPA/B second beta-propeller (B-prop_COPA_B_2nd)COPA/B second beta-propeller- Repeat
D [auth C],
P [auth J]		PF23953COPA/B TPR domain (TPR_COPA_B)COPA/B TPR domain- Repeat
D [auth C],
P [auth J]		PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
G,
J [auth K],
T [auth Q]		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
G,
J [auth K],
T [auth Q]		PF01602Adaptin N terminal region (Adaptin_N)Adaptin N terminal region- Repeat
G,
J [auth K],
T [auth Q]		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
I [auth Z],
K [auth L],
S [auth U],
U [auth S]		PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
E [auth D],
Q [auth N]		PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A,
M [auth H]		Coatomer subunit alpha
B [auth E],
N [auth O]		Coatomer subunit epsilon
C [auth B],
O [auth I]		Coatomer subunit beta
D [auth C],
P [auth J]		Coatomer subunit beta'
G,
J [auth K],
T [auth Q]		Coatomer subunit gamma-1
I [auth Z],
K [auth L],
S [auth U],
U [auth S]		Coatomer subunit zeta-1-
F,
H [auth R],
L [auth M],
R [auth P],
V [auth T]		ADP-ribosylation factor 1
E [auth D],
Q [auth N]		Coatomer subunit delta-

InterPro: Protein Family Classification InterPro Database Homepage

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