6MZJ

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs bound, sharpened map

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GP120_2nd	e6mzjA5	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	e6mzjA2	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	e6mzjA4	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)
A	GP41_1st	e6mzjA3	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 [auth B]	GP120_2nd	e6mzjB5	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)
D [auth B]	GP120_3rd	e6mzjB3	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)
D [auth B]	GP120_1st	e6mzjB4	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)
D [auth B]	GP41_1st	e6mzjB2	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 E]	GP120_2nd	e6mzjE5	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)
G [auth E]	GP120_3rd	e6mzjE3	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)
G [auth E]	GP120_1st	e6mzjE4	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)
G [auth E]	GP41_1st	e6mzjE2	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)
B [auth L]	V-set	e6mzjL1	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)
E [auth C]	V-set	e6mzjC1	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)
F [auth D]	V-set_8	e6mzjD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	V-set_8	e6mzjH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	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
B [auth L], E [auth C]	Fab VRC01, broadly Neutralizing antibody	L-KAPPA	Homo sapiens (human)	IGKV3-1101, IGKJ201, IGKJ202, IGKJ203, IGKJ204, IGKJ1S101, IGKJ301, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202507-0)
C [auth H], F [auth D]	Fab VRC01, broadly Neutralizing antibody	VH-CH1	Homo sapiens (human)	IGHV1-202, IGHJ101, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202507-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], E [auth C]	Light Chain	IGKV3	Kappa	426c ds-sosip d3	SAbDab (2025-02-28)
C [auth H], F [auth D]	Heavy Chain	IGHV1	-	426c ds-sosip d3	SAbDab (2025-02-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B], G [auth E]	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
A, D [auth B], G [auth E]	PF00517	Retroviral envelope protein (GP41)	Retroviral envelope protein	-	Family
B [auth L], E [auth C]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C [auth H], F [auth D]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B], G [auth E]	426c DS-SOSIP D3	structural molecule activity	viral process membrane fusion involved in viral entry into host cell 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 symbiont entry into host cell symbiont entry into host fusion of virus membrane with host endosome membrane membrane organization cellular component organization viral process membrane fusion involved in viral entry into host cell 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 symbiont entry into host cell symbiont entry into host fusion of virus membrane with host endosome membrane membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis protein localization 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 cellular macromolecule localization macromolecule localization receptor clustering positive regulation of protein localization regulation of receptor clustering regulation of protein localization to membrane positive regulation of cellular process 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 clathrin-dependent endocytosis 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	virion component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle virion component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell endosome host intracellular region
B [auth L], E [auth C]	VRC01GL light chain	-	-	cellular anatomical structure extracellular region
C [auth H], F [auth D]	VRC01GL heavy chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B], G [auth E]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, D [auth B], G [auth E]	IPR036377	Gp120 core superfamily	Homologous Superfamily
A, D [auth B], G [auth E]	IPR000328	Retroviral envelope protein GP41-like	Domain
A, D [auth B], G [auth E]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, D [auth B], G [auth E]	IPR036377	Gp120 core superfamily	Homologous Superfamily
A, D [auth B], G [auth E]	IPR000328	Retroviral envelope protein GP41-like	Domain
A, D [auth B], G [auth E]	IPR037527	Envelope glycoprotein Gp160	Family
B [auth L], E [auth C]	IPR003597	Immunoglobulin C1-set	Domain
B [auth L], E [auth C]	IPR050150	Immunoglobulin Variable Light Chain	Family
B [auth L], E [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth L], E [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L], E [auth C]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth L], E [auth C]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth L], E [auth C]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L], E [auth C]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth H], F [auth D]	IPR003597	Immunoglobulin C1-set	Domain
C [auth H], F [auth D]	IPR050199	Immunoglobulin Heavy Variable	Family
C [auth H], F [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth H], F [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H], F [auth D]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth H], F [auth D]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth H], F [auth D]	IPR007110	Immunoglobulin-like domain	Domain
C [auth H], F [auth D]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth H], F [auth D]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420