6MUF

Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.4 Angstrom

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth D]	d6mufd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth E]	d6mufe_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth H]	d6mufh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth H]	d6mufh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d6mufl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d6mufl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	GP41_1st	e6mufB1	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 D]	V-set_8	e6mufD1	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)
D [auth G]	GP120_2nd	e6mufG1	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 G]	GP120_3rd	e6mufG3	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 G]	GP120_1st	e6mufG2	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 [auth E]	V-set_3	e6mufE1	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)
E [auth H]	V-set_8	e6mufH1	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)
E [auth H]	C1-set_1	e6mufH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F [auth L]	C1-set	e6mufL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
F [auth L]	V-set_3	e6mufL1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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 D]	scFv 35O22	VH	Homo sapiens (human)	IGHV1-1801, IGHV1-1804, IGHJ101, IGHJ401, IGHJ502, IGHJ402, IGHJ4*03	V-DOMAIN VH	IG	FV-HEAVY_LAMBDA	IMGT (202449-0)
C [auth E]	scFv 35O22	V-LAMBDA	Homo sapiens (human)	IGLV2-1402, IGLV2-1802, IGLV2-2301, IGLV2-2302, IGLV2-2303, IGLJ101	V-DOMAIN V-LAMBDA	IG	FV-HEAVY_LAMBDA	IMGT (202449-0)
E [auth H]	Fab 3H109L	VH-CH1	Homo sapiens (human)	IGHV4-5901, IGHV4-5908, IGHV4-408, IGHJ301, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202449-0)
F [auth L]	Fab 3H109L	L-LAMBDA	Homo sapiens (human)	IGLV3-2101, IGLJ201, IGLJ701, IGLJ301, IGLC3*03	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202449-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth H]	Heavy Chain	IGHV4	-	envelope glycoprotein gp160	SAbDab (2024-12-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF00517	Retroviral envelope protein (GP41)	Retroviral envelope protein	-	Family
D [auth G]	PF00516	Envelope glycoprotein GP120 (GP120)	Envelope glycoprotein GP120	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Envelope glycoprotein gp160	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 establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of cellular process 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 establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of cellular process regulation of leukocyte activation establishment of T cell polarity positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion establishment or maintenance of cell polarity lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of establishment of T cell polarity positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of cellular process regulation of biological process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation establishment of cell polarity regulation of establishment of cell polarity immune system process regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation protein localization regulation of localization cellular localization regulation of protein localization positive regulation of receptor clustering 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 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-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation by virus of host process virus-mediated perturbation of host defense response modulation of process of another organism modulation by virus of host 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 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 transport of virus apoptotic process cell death programmed cell death viral gene expression viral protein processing	virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cell periphery plasma membrane membrane viral membrane viral envelope host cell plasma membrane
B [auth D]	35O22 scFv heavy chain portion	-	-	-
D [auth G]	Envelope glycoprotein gp160	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 establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of cellular process 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 establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of cellular process regulation of leukocyte activation establishment of T cell polarity positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion establishment or maintenance of cell polarity lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of establishment of T cell polarity positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of cellular process regulation of biological process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation establishment of cell polarity regulation of establishment of cell polarity immune system process regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation protein localization regulation of localization cellular localization regulation of protein localization positive regulation of receptor clustering 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 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-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation by virus of host process virus-mediated perturbation of host defense response modulation of process of another organism modulation by virus of host 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 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 transport of virus apoptotic process cell death programmed cell death viral gene expression viral protein processing	virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cell periphery plasma membrane membrane viral membrane viral envelope host cell plasma membrane
C [auth E]	35O22 scFv light chain portion	-	-	-
E [auth H]	3H109L Fab heavy chain	-	-	-
F [auth L]	3H109L Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.