9D98 | pdb_00009d98

Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with two gp120 protomers rotated, Population 5

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
M	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054493	3000071	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054493	3000071	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054493	3000071	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G, I, K	Heavy Chain	IGHV1	-	transmembrane protein gp41 \| surface protein gp120	SAbDab (2026-02-06)
H, J, L	Light Chain	IGKV1	Kappa	transmembrane protein gp41 \| surface protein gp120	SAbDab (2026-02-06)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
M, N, O	PF00047	Immunoglobulin domain (ig)	Immunoglobulin domain	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ...	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Surface protein 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
D, E, F	Transmembrane protein gp41	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	virion component viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part virion membrane host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle virion component viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part 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
G, I, K	VRC34.01 Fab heavy chain	-	-	-
H, J, L	VRC34.01 Fab light chain	-	-	-
M, N, O	T-cell surface glycoprotein CD4	molecular transducer activity coreceptor activity signaling receptor activity protein-containing complex binding binding MHC protein complex binding MHC class II protein complex binding immunoglobulin binding interleukin-16 binding protein binding cytokine binding protein tyrosine kinase binding kinase binding enzyme binding molecular transducer activity coreceptor activity signaling receptor activity protein-containing complex binding binding MHC protein complex binding MHC class II protein complex binding immunoglobulin binding interleukin-16 binding protein binding cytokine binding protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding identical protein binding transmembrane signaling receptor activity virus receptor activity exogenous protein binding signaling receptor binding MHC class II protein binding MHC protein binding interleukin-16 receptor activity cytokine receptor activity immune receptor activity structural molecule activity extracellular matrix structural constituent protein homodimerization activity protein dimerization activity lipid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication cellular process positive regulation of signaling maintenance of protein location localization cellular localization maintenance of protein location in cell macromolecule localization intracellular protein localization maintenance of location maintenance of location in cell immune response immune system process adaptive immune response biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction developmental process multicellular organismal process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation cell differentiation anatomical structure development T cell differentiation leukocyte differentiation interleukin-15-mediated signaling pathway cell surface receptor signaling pathway response to cytokine cellular response to interleukin-15 cytokine-mediated signaling pathway response to peptide response to chemical cellular response to cytokine stimulus response to interleukin-15 regulation of leukocyte activation regulation of cell activation regulation of T cell activation regulation of immune system process regulation of multicellular organismal process regulation of lymphocyte activation myeloid leukocyte differentiation regulation of leukocyte differentiation positive regulation of monocyte differentiation regulation of developmental process regulation of cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation positive regulation of hemopoiesis monocyte differentiation positive regulation of immune system process regulation of multicellular organismal development regulation of monocyte differentiation regulation of myeloid cell differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of multicellular organismal process positive regulation of leukocyte differentiation response to amine response to methamphetamine hydrochloride response to nitrogen compound cell adhesion regulation of localization regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport regulation of calcium ion transport into cytosol transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport monoatomic cation transmembrane transport regulation of calcium ion transmembrane transport positive regulation of monoatomic ion transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport regulation of biological quality monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport positive regulation of cytosolic calcium ion concentration establishment of localization transmembrane transport positive regulation of calcium ion transport into cytosol regulation of transmembrane transport positive regulation of transport regulation of cellular localization regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport calcium ion transport into cytosol response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium response to bacterium response to stress response to external biotic stimulus response to lipid cellular response to ionomycin response to fatty acid response to oxygen-containing compound cellular response to ether cellular response to oxygen-containing compound cellular response to fatty acid cellular response to chemical stimulus response to ether cellular response to lipid response to ionomycin positive regulation of cell population proliferation positive regulation of cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion leukocyte proliferation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell proliferation regulation of mononuclear cell proliferation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains helper T cell enhancement of adaptive immune response positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of adaptive immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune response regulation of immune response positive regulation of adaptive immune response immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway activation of immune response T cell selection response to alcohol response to ethanol response to granulocyte macrophage colony-stimulating factor cellular response to granulocyte macrophage colony-stimulating factor stimulus macrophage differentiation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of interleukin-2 production interleukin-2 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of interleukin-2 production regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process response to nutrient levels response to vitamin D response to nutrient response to vitamin cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway response to estradiol	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane membrane-enclosed lumen endomembrane system intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex T cell receptor complex receptor complex membrane microdomain membrane raft organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane early endosome endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, B, C	IPR036377	Gp120 core superfamily	Homologous Superfamily
A, B, C	IPR000328	Retroviral envelope protein GP41-like	Domain
A, B, C	IPR037527	Envelope glycoprotein Gp160	Family
D, E, F	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
D, E, F	IPR036377	Gp120 core superfamily	Homologous Superfamily
D, E, F	IPR000328	Retroviral envelope protein GP41-like	Domain
M, N, O	IPR021963	T cell CD4 receptor C-terminal region	Domain
M, N, O	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
M, N, O	IPR013106	Immunoglobulin V-set domain	Domain
M, N, O	IPR000973	T-cell surface antigen CD4	Family
M, N, O	IPR003599	Immunoglobulin domain subtype	Domain
M, N, O	IPR008424	Immunoglobulin C2-set	Domain
M, N, O	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
M, N, O	IPR015274	CD4, extracellular	Domain
M, N, O	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
M, N, O	IPR007110	Immunoglobulin-like domain	Domain
M, N, O	IPR003598	Immunoglobulin subtype 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
M, N, O	Pharos: P01730	Duchenne muscular dystrophy diabetes mellitus AIDS-Related Opportunistic Infections coronary artery disease lymphopenia cryptococcosis malignant glioma neutropenia Duchenne and Becker muscular dystrophy ovarian disease pneumonia adult acute respiratory distress syndrome glioblastoma rheumatoid arthritis hepatitis B virus infection Duchenne muscular dystrophy diabetes mellitus AIDS-Related Opportunistic Infections coronary artery disease lymphopenia cryptococcosis malignant glioma neutropenia Duchenne and Becker muscular dystrophy ovarian disease pneumonia adult acute respiratory distress syndrome glioblastoma rheumatoid arthritis hepatitis B virus infection severe combined immunodeficiency arthritic joint disease HIV infectious disease syphilis autoimmune disease IgA glomerulonephritis toxoplasmosis breast carcinoma influenza uveitis candidiasis kidney disease vertebral column disease colorectal cancer lung carcinoma COVID-19 lymphoproliferative syndrome cutaneous lupus erythematosus measles diarrheal disease obesity disorder peripheral neuropathy prostate disease agammaglobulinemia heart disease rhinitis allergic disease hepatitis C virus infection skin disease asthma hypereosinophilic syndrome tetanus Becker muscular dystrophy inborn carbohydrate metabolic disorder tuberculosis breast disease interstitial lung disease vaccinia colitis leishmaniasis congenital T-cell immunodeficiency lymphatic system disease Crohn disease malaria demyelinating disease Okt4 epitope deficiency pneumocystosis encephalitis retinitis AIDS helminthiasis sarcoidosis anemia herpes zoster subependymal giant cell astrocytoma atherosclerosis hypertensive disorder thrombocytopenia bone marrow disease infectious meningitis uterine disease cancer invasive ductal breast carcinoma vasculitis colonic disease liver disease

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.