6NF2 | pdb_00006nf2

Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody 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)
R	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	gp120 core	8080371	3001390	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)
X	Lys	e6nf2X1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
P	Lys	e6nf2P1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
L	PDEase_I	e6nf2L1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: PDEase_I	ECOD (v295.2)
W	Lys	e6nf2W1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
O	Lys	e6nf2O1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
H	PDEase_I	e6nf2H1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: PDEase_I	ECOD (v295.2)
T	Lys	e6nf2T1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
K	Lys	e6nf2K1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
F	Lys	e6nf2F1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
S	Lys	e6nf2S1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
J	Lys	e6nf2J1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
E	Lys	e6nf2E1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
U	Lys	e6nf2U1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
M	Lys	e6nf2M1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
D	Lys	e6nf2D1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
V	Lys	e6nf2V1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
N	Lys	e6nf2N1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
C	Lys	e6nf2C1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
R	Lys	e6nf2R1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
I	Lys	e6nf2I1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
B	Lys	e6nf2B1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
Q	Lys	e6nf2Q1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
G	Lys	e6nf2G1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)
A	Lys	e6nf2A1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lys	ECOD (v295.2)

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
L, P, X	Fab 0PV-c.01	L-KAPPA	Homo sapiens (human)	IGKV2-4001, IGKV2D-4001, IGKJ401, IGKJ402, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202633-0)
H, O, W	Fab 0PV-c.01	VH-CH1	Homo sapiens (human)	IGHV4-6101, IGHV4-6108, IGHV4-408, IGHJ101, IGHG103, IGHG108, IGHG1*06	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202633-0)
F, K, T	Fab PGT122	L-LAMBDA	Homo sapiens (human)	IGLV3-2101, IGLV3-2102, IGLJ302, IGLC303	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202633-0)
E, J, S	Fab PGT122	VH-CH1	Homo sapiens (human)	IGHV4-5902, IGHJ301, IGHG103, IGHG108, IGHG1*06	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202633-0)
D, M, U	Fab VRC03	L-KAPPA	Homo sapiens (human)	IGKV3-1101, IGKV3D-1101, IGKV3D-1103, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202633-0)
C, N, V	Fab VRC03	VH-CH1	Homo sapiens (human)	IGHV1-202, IGHV1-4604, IGHJ301, IGHJ302, IGHJ502, IGHJ601, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202633-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
L, P, X	Light Chain	IGKV2	Kappa	envelope glycoprotein gp41	SAbDab (2026-08-28)
H, O, W	Heavy Chain	IGHV4	-	envelope glycoprotein gp41	SAbDab (2026-08-28)
E, J, S	Heavy Chain	IGHV4	-	envelope glycoprotein gp120	SAbDab (2026-08-28)
D, M, U	Light Chain	IGKV3	Kappa	envelope glycoprotein gp120	SAbDab (2026-08-28)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
L, P, X	0PV-c.01 Light Chain	-	-	-
H, O, W	0PV-c.01 Heavy Chain	-	-	-
F, K, T	PGT122 Light Chain	-	-	-
E, J, S	PGT122 Heavy Chain	-	-	-
D, M, U	VRC03 Light Chain	-	-	-
C, N, V	VRC03 Heavy Chain	-	-	-
B, I, R	Envelope glycoprotein gp41	structural molecule activity identical protein binding protein binding binding	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 symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism	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
A, G, Q	Envelope glycoprotein gp120	structural molecule activity identical protein binding protein binding binding	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 symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism	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
B, I, R	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
B, I, R	IPR036377	Gp120 core superfamily	Homologous Superfamily
B, I, R	IPR000328	Retroviral envelope protein GP41-like	Domain
B, I, R	IPR037527	Envelope glycoprotein Gp160	Family
A, G, Q	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, G, Q	IPR036377	Gp120 core superfamily	Homologous Superfamily
A, G, Q	IPR000328	Retroviral envelope protein GP41-like	Domain
A, G, Q	IPR037527	Envelope glycoprotein Gp160	Family

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.