8D4D | pdb_00008d4d

gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
R [auth O]SCOP2B SuperfamilySNARE-like 8082711 3001113 SCOP2B (2022-06-29)
I [auth S]SCOP2B SuperfamilySNARE-like 8082711 3001113 SCOP2B (2022-06-29)
H [auth M]SCOP2B Superfamilymu adaptin domain-like 8083652 3000810 SCOP2B (2022-06-29)
Q [auth J]SCOP2B Superfamilymu adaptin domain-like 8083652 3000810 SCOP2B (2022-06-29)
F [auth G]SCOP2B SuperfamilyARM repeat-like 8078176 3000116 SCOP2B (2022-06-29)
O [auth E]SCOP2B SuperfamilyARM repeat-like 8078176 3000116 SCOP2B (2022-06-29)
E [auth B]SCOP2B SuperfamilyARM repeat-like 8082787 3000116 SCOP2B (2022-06-29)
N [auth A]SCOP2B SuperfamilyARM repeat-like 8082787 3000116 SCOP2B (2022-06-29)
A [auth C]SCOP2B SuperfamilyRas-like P-loop GTPases 8089848 3002022 SCOP2B (2022-06-29)
K [auth F]SCOP2B SuperfamilyRas-like P-loop GTPases 8089848 3002022 SCOP2B (2022-06-29)
J [auth D]SCOP2B SuperfamilyRas-like P-loop GTPases 8089848 3002022 SCOP2B (2022-06-29)
B [auth H]SCOP2B SuperfamilyRas-like P-loop GTPases 8089848 3002022 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
R [auth O]Polyketide_cyc2e8d4dO1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
I [auth S]Polyketide_cyc2e8d4dS1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
H [auth M]Polyketide_cyc2e8d4dM1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
Q [auth J]Polyketide_cyc2e8d4dJ1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
F [auth G]Polyketide_cyc2e8d4dG1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
O [auth E]Polyketide_cyc2e8d4dE1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
E [auth B]Polyketide_cyc2e8d4dB1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
N [auth A]Polyketide_cyc2e8d4dA1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
L [auth K]Polyketide_cyc2e8d4dK1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
G [auth L]GP120e8d4dL01 A: alpha bundlesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: GP120ECOD (develop294)
C [auth N]Polyketide_cyc2e8d4dN1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
A [auth C]Polyketide_cyc2e8d4dC1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
K [auth F]Polyketide_cyc2e8d4dF1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
J [auth D]Polyketide_cyc2e8d4dD1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)
B [auth H]Polyketide_cyc2e8d4dH1 A: alpha bundlesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Polyketide_cyc2ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth S],
R [auth O]		PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
H [auth M],
Q [auth J]		PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
H [auth M],
Q [auth J]		PF00928Adaptor complexes medium subunit family (Adap_comp_sub)Adaptor complexes medium subunit family- Family
F [auth G],
O [auth E]		PF01602Adaptin N terminal region (Adaptin_N)Adaptin N terminal region- Repeat
A [auth C],
B [auth H],
J [auth D],
K [auth F]		PF00025ADP-ribosylation factor family (Arf)ADP-ribosylation factor familyPfam combines a number of different Prosite families together Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I [auth S],
R [auth O]		AP-1 complex subunit sigma-3
H [auth M],
Q [auth J]		AP-1 complex subunit mu-1
F [auth G],
O [auth E]		AP-1 complex subunit gamma-1
E [auth B],
N [auth A]		AP-1 complex subunit beta-1
D [auth Y],
M [auth P]		HLA class I histocompatibility antigen, A alpha chain
C [auth N],
G [auth L],
L [auth K],
P [auth I]		Protein Nef
A [auth C],
B [auth H],
J [auth D],
K [auth F]		ADP-ribosylation factor 1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I [auth S],
R [auth O]		IPR016635Adaptor protein complex, sigma subunitFamily
I [auth S],
R [auth O]		IPR011012Longin-like domain superfamilyHomologous Superfamily
I [auth S],
R [auth O]		IPR044733AP-1 complex subunit sigmaFamily
I [auth S],
R [auth O]		IPR000804Clathrin adaptor complex, small chainConserved Site
I [auth S],
R [auth O]		IPR022775AP complex, mu/sigma subunitDomain
H [auth M],
Q [auth J]		IPR050431Adaptor complexes medium subunitFamily
H [auth M],
Q [auth J]		IPR011012Longin-like domain superfamilyHomologous Superfamily
H [auth M],
Q [auth J]		IPR022775AP complex, mu/sigma subunitDomain
H [auth M],
Q [auth J]		IPR036168AP-2 complex subunit mu, C-terminal superfamilyHomologous Superfamily
H [auth M],
Q [auth J]		IPR028565Mu homology domainDomain
H [auth M],
Q [auth J]		IPR018240Clathrin adaptor, mu subunit, conserved siteConserved Site
H [auth M],
Q [auth J]		IPR001392Clathrin adaptor, mu subunitFamily
F [auth G],
O [auth E]		IPR016024Armadillo-type foldHomologous Superfamily
F [auth G],
O [auth E]		IPR017107Adaptor protein complex AP-1, gamma subunitFamily
F [auth G],
O [auth E]		IPR011989Armadillo-like helicalHomologous Superfamily
F [auth G],
O [auth E]		IPR008153Gamma-adaptin ear (GAE) domainDomain
F [auth G],
O [auth E]		IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
F [auth G],
O [auth E]		IPR013041Clathrin adaptor, appendage, Ig-like subdomain superfamilyHomologous Superfamily
F [auth G],
O [auth E]		IPR050840Adaptor Complexes Large SubunitFamily
F [auth G],
O [auth E]		IPR008152Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomainDomain
E [auth B],
N [auth A]		IPR016024Armadillo-type foldHomologous Superfamily
E [auth B],
N [auth A]		IPR013037Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomainHomologous Superfamily
E [auth B],
N [auth A]		IPR000225ArmadilloRepeat
E [auth B],
N [auth A]		IPR026739AP complex subunit betaFamily
E [auth B],
N [auth A]		IPR011989Armadillo-like helicalHomologous Superfamily
E [auth B],
N [auth A]		IPR012295TBP domain superfamilyHomologous Superfamily
E [auth B],
N [auth A]		IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
E [auth B],
N [auth A]		IPR015151Beta-adaptin appendage, C-terminal subdomainDomain
E [auth B],
N [auth A]		IPR013041Clathrin adaptor, appendage, Ig-like subdomain superfamilyHomologous Superfamily
E [auth B],
N [auth A]		IPR008152Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomainDomain
E [auth B],
N [auth A]		IPR009028Coatomer/calthrin adaptor appendage, C-terminal subdomainHomologous Superfamily
E [auth B],
N [auth A]		IPR016342AP-1/2/4 complex subunit betaFamily
D [auth Y],
M [auth P]		IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
D [auth Y],
M [auth P]		IPR010579MHC class I, alpha chain, C-terminalDomain
D [auth Y],
M [auth P]		IPR011162MHC classes I/II-like antigen recognition proteinHomologous Superfamily
D [auth Y],
M [auth P]		IPR001039MHC class I alpha chain, alpha1 alpha2 domainsDomain
D [auth Y],
M [auth P]		IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
D [auth Y],
M [auth P]		IPR013783Immunoglobulin-like foldHomologous Superfamily
D [auth Y],
M [auth P]		IPR007110Immunoglobulin-like domainDomain
D [auth Y],
M [auth P]		IPR050208Antigen-presenting and immune regulatory MHC class I-relatedFamily
D [auth Y],
M [auth P]		IPR003597Immunoglobulin C1-setDomain
D [auth Y],
M [auth P]		IPR011161MHC class I-like antigen recognition-likeDomain
D [auth Y],
M [auth P]		IPR037055MHC class I-like antigen recognition-like superfamilyHomologous Superfamily
C [auth N],
G [auth L],
L [auth K],
P [auth I]		IPR001558HIV negative factor NefFamily
C [auth N],
G [auth L],
L [auth K],
P [auth I]		IPR027481HIV-1 Nef protein, core domain superfamilyHomologous Superfamily
C [auth N],
G [auth L],
L [auth K],
P [auth I]		IPR027480HIV-1 Nef protein, anchor domain superfamilyHomologous Superfamily
A [auth C],
B [auth H],
J [auth D],
K [auth F]		IPR045872ADP-ribosylation factor 1-5Family
A [auth C],
B [auth H],
J [auth D],
K [auth F]		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
A [auth C],
B [auth H],
J [auth D],
K [auth F]		IPR005225Small GTP-binding domainDomain
A [auth C],
B [auth H],
J [auth D],
K [auth F]		IPR024156Small GTPase superfamily, ARF typeFamily
A [auth C],
B [auth H],
J [auth D],
K [auth F]		IPR006689Small GTPase superfamily, ARF/SAR typeFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
I [auth S],
R [auth O]		Pharos:  Q96PC3
E [auth B],
N [auth A]		Pharos:  Q10567
D [auth Y],
M [auth P]		Pharos:  P04439
A [auth C],
B [auth H],
J [auth D],
K [auth F]		Pharos:  P84077

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

ChainsResource LinkGroupSubgroupProtein
mpstrucMONOTOPIC MEMBRANE PROTEINSADP-Ribosylation FactorsADP-ribosylation factor (ARF1)/AP-1 complex, with HIV1-Nef and MHC-I lipopeptide, narrow membrane tubes