3JCB | pdb_00003jcb

Structure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054493	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054739	3000071	SCOP2B (2022-06-29)
F [auth I]	SCOP2 Family	gp120 core	8096749	4002534	SCOP2 (2022-06-29)
F [auth I]	SCOP2 Superfamily	gp120 core	8096750	3001390	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	gp120 core	8096750	3001390	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	gp120 core	8096750	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)
D	C2-set	e3jcbD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C2-set	ECOD (1.6)
D	V-set_9	e3jcbD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)
C	V-set_8	e3jcbC2	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	C1-set_1	e3jcbC1	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)
B	C1-set	e3jcbB1	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)
B	V-set_3	e3jcbB2	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)
F [auth I]	GP120_2nd	e3jcbI1	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)
F [auth I]	GP120_3rd	e3jcbI3	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)
F [auth I]	GP120_1st	e3jcbI2	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)
E	GP120_2nd	e3jcbE3	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)
E	GP120_3rd	e3jcbE2	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)
E	GP120_1st	e3jcbE1	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	GP120_2nd	e3jcbA3	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	e3jcbA1	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	e3jcbA2	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)

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
D	T-cell surface glycoprotein CD4	1V-1C-LIKE	Homo sapiens (human)	CD4	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	1V-1C-LIKE	IMGT (202546-0)
C	36D5 mAb, neutralizing	VH-CH1	Homo sapiens (human)	IGHV4-5902, IGHJ301, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202546-0)
B	36D5 mAb, neutralizing	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 (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV4	-	envelope glycoprotein gp120	SAbDab (2025-11-28)
B	Light Chain	IGLV3	Lambda	envelope glycoprotein gp120	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF05790	Immunoglobulin C2-set domain (C2-set)	Immunoglobulin C2-set domain		Domain
D	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
A, E, F [auth I]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	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 regulation of calcium ion transport regulation of localization transport regulation of transport regulation of monoatomic ion transport establishment of localization metal ion transport calcium ion transport monoatomic ion transport regulation of metal ion transport monoatomic cation transport 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 positive regulation of phosphorylation regulation of catalytic activity positive regulation of phosphate metabolic process regulation of transferase activity positive regulation of metabolic process positive regulation of molecular function phosphate-containing compound metabolic process phosphorus metabolic process positive regulation of phosphorus metabolic process phosphorylation positive regulation of catalytic activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity metabolic process regulation of phosphorus metabolic process regulation of phosphorylation regulation of metabolic process 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 positive regulation of cation transmembrane transport positive regulation of calcium ion transport regulation of calcium ion transport into cytosol monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane 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 positive regulation of monoatomic ion transmembrane transport regulation of biological quality calcium ion transmembrane import into cytosol positive regulation of cytosolic calcium ion concentration 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 regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of primary metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity protein modification process positive regulation of protein phosphorylation protein phosphorylation regulation of protein metabolic process primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process macromolecule modification macromolecule metabolic process positive regulation of viral life cycle positive regulation of viral process modulation by symbiont of entry into host regulation of viral entry into host cell regulation of viral life cycle regulation of viral process positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction 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 positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade 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 biosynthetic process regulation of cytokine production cytokine production regulation of biosynthetic process regulation of interleukin-2 production interleukin-2 production 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 positive regulation of cytokine production 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 positive regulation of DNA-templated transcription RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription 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
C	Antibody 36D5 heavy chain	-	-	-
B	Antibody 36D5 light chain	-	-	-
A, E, F [auth I]	Envelope glycoprotein gp120	-	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host	virion component viral membrane viral envelope virion membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR021963	T cell CD4 receptor C-terminal region	Domain
D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D	IPR013106	Immunoglobulin V-set domain	Domain
D	IPR000973	T-cell surface antigen CD4	Family
D	IPR003599	Immunoglobulin domain subtype	Domain
D	IPR008424	Immunoglobulin C2-set	Domain
D	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
D	IPR015274	CD4, extracellular	Domain
D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D	IPR007110	Immunoglobulin-like domain	Domain
D	IPR003598	Immunoglobulin subtype 2	Domain
A, E, F [auth I]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, E, F [auth I]	IPR036377	Gp120 core superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

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

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.