6CM9 | pdb_00006cm9

Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
H [auth S]SCOP2B SuperfamilySNARE-like 8082711 3001113 SCOP2B (2022-06-29)
G [auth M]SCOP2B Superfamilymu adaptin domain-like 8083652 3000810 SCOP2B (2022-06-29)
E [auth G]SCOP2 FamilyClathrin adaptor core protein 8078175 4001978 SCOP2 (2022-06-29)
E [auth G]SCOP2 SuperfamilyARM repeat-like 8078176 3000116 SCOP2 (2022-06-29)
F [auth H]SCOP2B SuperfamilyRas-like P-loop GTPases 8089848 3002022 SCOP2B (2022-06-29)
D [auth C]SCOP2B SuperfamilyRas-like P-loop GTPases 8089848 3002022 SCOP2B (2022-06-29)
C [auth B]SCOP2B SuperfamilyARM repeat-like 8082787 3000116 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
H [auth S]Histonee6cm9S1 A: alpha bundlesX: PriB N-terminal domain-likeH: ADP-ribosylationT: ADP-ribosylationF: HistoneECOD (develop294)
G [auth M]Histonee6cm9M1 A: alpha bundlesX: PriB N-terminal domain-likeH: ADP-ribosylationT: ADP-ribosylationF: HistoneECOD (develop294)
E [auth G]Histonee6cm9G1 A: alpha bundlesX: PriB N-terminal domain-likeH: ADP-ribosylationT: ADP-ribosylationF: HistoneECOD (develop294)
F [auth H]Anoctamine6cm9H1 A: alpha bundlesX: PriB N-terminal domain-likeH: gp11/gp12 receptor-binding domainT: gp11/gp12 receptor-binding domainF: AnoctaminECOD (develop294)
D [auth C]Histonee6cm9C1 A: alpha bundlesX: PriB N-terminal domain-likeH: ADP-ribosylationT: ADP-ribosylationF: HistoneECOD (develop294)
C [auth B]Histonee6cm9B1 A: alpha bundlesX: PriB N-terminal domain-likeH: ADP-ribosylationT: ADP-ribosylationF: HistoneECOD (develop294)
I [auth N]Histonee6cm9N1 A: alpha bundlesX: PriB N-terminal domain-likeH: ADP-ribosylationT: ADP-ribosylationF: HistoneECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
H [auth S]3.30.450.60 Alpha Beta 2-Layer Sandwich Beta-Lactamase CATH (4.3.0)
G [auth M]3.30.450.60 Alpha Beta 2-Layer Sandwich Beta-Lactamase CATH (4.3.0)
E [auth G]1.25.10.10 Mainly Alpha Alpha Horseshoe Leucine-rich Repeat Variant Leucine-rich Repeat VariantCATH (4.3.0)
F [auth H]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
D [auth C]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
C [auth B]1.25.10.10 Mainly Alpha Alpha Horseshoe Leucine-rich Repeat Variant Leucine-rich Repeat VariantCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
H [auth S]PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
G [auth M]PF01217Clathrin adaptor complex small chain (Clat_adaptor_s)Clathrin adaptor complex small chainDomain
G [auth M]PF00928Adaptor complexes medium subunit family (Adap_comp_sub)Adaptor complexes medium subunit family- Family
E [auth G]PF01602Adaptin N terminal region (Adaptin_N)Adaptin N terminal region- Repeat
D [auth C],
F [auth H]		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
H [auth S]AP-1 complex subunit sigma-3
G [auth M]AP-1 complex subunit mu-1
E [auth G]AP-1 complex subunit gamma-1
D [auth C],
F [auth H]		ADP-ribosylation factor 1
C [auth B]AP-1 complex subunit beta-1
A [auth L],
B [auth T],
I [auth N]		Bone marrow stromal antigen 2, Protein Nef chimera

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
H [auth S]IPR016635Adaptor protein complex, sigma subunitFamily
H [auth S]IPR011012Longin-like domain superfamilyHomologous Superfamily
H [auth S]IPR044733AP-1 complex subunit sigmaFamily
H [auth S]IPR000804Clathrin adaptor complex, small chainConserved Site
H [auth S]IPR022775AP complex, mu/sigma subunitDomain
G [auth M]IPR050431Adaptor complexes medium subunitFamily
G [auth M]IPR011012Longin-like domain superfamilyHomologous Superfamily
G [auth M]IPR022775AP complex, mu/sigma subunitDomain
G [auth M]IPR036168AP-2 complex subunit mu, C-terminal superfamilyHomologous Superfamily
G [auth M]IPR028565Mu homology domainDomain
G [auth M]IPR018240Clathrin adaptor, mu subunit, conserved siteConserved Site
G [auth M]IPR001392Clathrin adaptor, mu subunitFamily
E [auth G]IPR016024Armadillo-type foldHomologous Superfamily
E [auth G]IPR017107Adaptor protein complex AP-1, gamma subunitFamily
E [auth G]IPR011989Armadillo-like helicalHomologous Superfamily
E [auth G]IPR008153Gamma-adaptin ear (GAE) domainDomain
E [auth G]IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
E [auth G]IPR013041Clathrin adaptor, appendage, Ig-like subdomain superfamilyHomologous Superfamily
E [auth G]IPR050840Adaptor Complexes Large SubunitFamily
E [auth G]IPR008152Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomainDomain
D [auth C],
F [auth H]		IPR045872ADP-ribosylation factor 1-5Family
D [auth C],
F [auth H]		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
D [auth C],
F [auth H]		IPR005225Small GTP-binding domainDomain
D [auth C],
F [auth H]		IPR024156Small GTPase superfamily, ARF typeFamily
D [auth C],
F [auth H]		IPR006689Small GTPase superfamily, ARF/SAR typeFamily
C [auth B]IPR016024Armadillo-type foldHomologous Superfamily
C [auth B]IPR013037Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomainHomologous Superfamily
C [auth B]IPR000225ArmadilloRepeat
C [auth B]IPR026739AP complex subunit betaFamily
C [auth B]IPR011989Armadillo-like helicalHomologous Superfamily
C [auth B]IPR012295TBP domain superfamilyHomologous Superfamily
C [auth B]IPR002553Clathrin/coatomer adaptor, adaptin-like, N-terminalDomain
C [auth B]IPR015151Beta-adaptin appendage, C-terminal subdomainDomain
C [auth B]IPR013041Clathrin adaptor, appendage, Ig-like subdomain superfamilyHomologous Superfamily
C [auth B]IPR008152Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomainDomain
C [auth B]IPR009028Coatomer/calthrin adaptor appendage, C-terminal subdomainHomologous Superfamily
C [auth B]IPR016342AP-1/2/4 complex subunit betaFamily
A [auth L],
B [auth T],
I [auth N]		IPR024886Bone marrow stromal antigen 2Family
A [auth L],
B [auth T],
I [auth N]		IPR001558HIV negative factor NefFamily
A [auth L],
B [auth T],
I [auth N]		IPR027481HIV-1 Nef protein, core domain superfamilyHomologous Superfamily
A [auth L],
B [auth T],
I [auth N]		IPR027480HIV-1 Nef protein, anchor domain superfamilyHomologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
H [auth S]Pharos:  Q96PC3
D [auth C],
F [auth H]		Pharos:  P84077
C [auth B]Pharos:  Q10567
A [auth L],
B [auth T],
I [auth N]		Pharos:  Q10589