6VPX | pdb_00006vpx

Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	gp120 core	8097350	3001390	SCOP2B (2022-06-29)
C	SCOP2 Family	gp120 core	8097349	4002534	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	gp120 core	8097350	3001390	SCOP2 (2022-06-29)
B [auth E]	SCOP2B Superfamily	gp120 core	8097350	3001390	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Virus ectodomain	8097216	3001628	SCOP2B (2022-06-29)
E [auth B]	SCOP2 Family	Virus ectodomain	8097215	4003841	SCOP2 (2022-06-29)
E [auth B]	SCOP2 Superfamily	Virus ectodomain	8097216	3001628	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Virus ectodomain	8097216	3001628	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GP120_2nd	e6vpxA3	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
A	GP120_3rd	e6vpxA2	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
A	GP120_1st	e6vpxA1	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
C	GP120_2nd	e6vpxC1	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
C	GP120_3rd	e6vpxC2	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
C	GP120_1st	e6vpxC3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
B [auth E]	GP120_2nd	e6vpxE2	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
B [auth E]	GP120_3rd	e6vpxE1	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
B [auth E]	GP120_1st	e6vpxE3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
F	GP41_1st	e6vpxF1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
E [auth B]	GP41_1st	e6vpxB1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
D	GP41_1st	e6vpxD1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
G [auth H]	V-set_12	e6vpxH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
M	V-set_12	e6vpxM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
J [auth K]	V-set_12	e6vpxK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
H [auth L]	V-set_3	e6vpxL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
N [auth O]	V-set_3	e6vpxO1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
K [auth N]	V-set_3	e6vpxN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
P	V-set_12	e6vpxP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
Q	V-set	e6vpxQ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
G [auth H], J [auth K], M	Fab 10E8	VH	Homo sapiens (human)	IGHV3-1501, IGHV3-1505, IGHJ2*01	V-DOMAIN VH	IG	FV-HEAVY_LAMBDA	IMGT (202538-0)
H [auth L], K [auth N], N [auth O]	Fab 10E8	V-LAMBDA	Homo sapiens (human)	IGLV3-1901, IGLJ201, IGLJ302, IGLJ301	V-DOMAIN V-LAMBDA	IG	FV-HEAVY_LAMBDA	IMGT (202538-0)
P	Fab PGT151	VH	Homo sapiens (human)	IGHV3-3009, IGHV3-3010, IGHJ6*01	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202538-0)
Q	Fab PGT151	V-KAPPA	Homo sapiens (human)	IGKV2D-2902, IGKJ401, IGKJ4*02	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202538-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth H], J [auth K], M	Heavy Chain	IGHV3	-	mper peptide, mper peptide \| envelope glycoprotein gp120, mper peptide \| envelope glycoprotein gp120 \| envelope glycoprotein gp41	SAbDab (2025-10-03)
H [auth L], K [auth N], N [auth O]	Light Chain	IGLV3	Lambda	mper peptide, mper peptide \| envelope glycoprotein gp120, mper peptide \| envelope glycoprotein gp120 \| envelope glycoprotein gp41	SAbDab (2025-10-03)
P	Heavy Chain	IGHV3	-	envelope glycoprotein gp41 \| envelope glycoprotein gp120 \| envelope glycoprotein gp41	SAbDab (2025-10-03)
Q	Light Chain	IGKV2	Kappa	envelope glycoprotein gp41 \| envelope glycoprotein gp120 \| envelope glycoprotein gp41	SAbDab (2025-10-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth E], C	PF00516	Envelope glycoprotein GP120 (GP120)	Envelope glycoprotein GP120	The envelope glycoprotein Gp160 of HIV1 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. The entry of HIV requires interaction of viral GP120 with the CD4 glycoprotein (Swiss:P01730) and a chemokine receptor on the cell s ...	The envelope glycoprotein Gp160 of HIV1 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. The entry of HIV requires interaction of viral GP120 with the CD4 glycoprotein (Swiss:P01730) and a chemokine receptor on the cell surface [1]. Gp160 us proteolytically cleaved n the trans-Golgi and activated by cellular furin or furin-like proteases to produce gp120 and gp41 [1,2].	Domain
D, E [auth B], F	PF00517	Retroviral envelope protein (GP41)	Retroviral envelope protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth E], C	Envelope glycoprotein gp120	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of receptor clustering biological regulation positive regulation of biological process positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization receptor clustering positive regulation of protein localization intracellular protein localization regulation of receptor clustering regulation of protein localization to membrane positive regulation of cellular process virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction plasma membrane raft distribution regulation of cellular component organization positive regulation of cellular component organization plasma membrane raft polarization plasma membrane organization membrane raft organization endomembrane system organization membrane raft distribution plasma membrane raft localization membrane raft polarization regulation of plasma membrane raft polarization membrane raft localization regulation of plasma membrane organization positive regulation of plasma membrane raft polarization import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral protein processing	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane
D, E [auth B], F	Envelope glycoprotein gp41	structural molecule activity	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion membrane
G [auth H], J [auth K], M	Antibody 10E8 Fab heavy chain	-	-	-
H [auth L], K [auth N], N [auth O]	Antibody 10E8 Fab light chain	-	-	-
P	Antibody PGT151 Fab heavy chain	-	-	-
Q	Antibody PGT151 Fab light chain	-	-	-
I [auth G], L [auth I], O [auth J]	MPER peptide	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of receptor clustering biological regulation positive regulation of biological process positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization receptor clustering positive regulation of protein localization intracellular protein localization regulation of receptor clustering regulation of protein localization to membrane positive regulation of cellular process virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction plasma membrane raft distribution regulation of cellular component organization positive regulation of cellular component organization plasma membrane raft polarization plasma membrane organization membrane raft organization endomembrane system organization membrane raft distribution plasma membrane raft localization membrane raft polarization regulation of plasma membrane raft polarization membrane raft localization regulation of plasma membrane organization positive regulation of plasma membrane raft polarization import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral protein processing	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth E], C	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, B [auth E], C	IPR036377	Gp120 core superfamily	Homologous Superfamily
A, B [auth E], C	IPR000328	Retroviral envelope protein GP41-like	Domain
A, B [auth E], C	IPR037527	Envelope glycoprotein Gp160	Family
D, E [auth B], F	IPR000328	Retroviral envelope protein GP41-like	Domain
I [auth G], L [auth I], O [auth J]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
I [auth G], L [auth I], O [auth J]	IPR036377	Gp120 core superfamily	Homologous Superfamily
I [auth G], L [auth I], O [auth J]	IPR000328	Retroviral envelope protein GP41-like	Domain
I [auth G], L [auth I], O [auth J]	IPR037527	Envelope glycoprotein Gp160	Family