Annotations: 7LU9

Cryo-EM structure of DH851.3 bound to HIV-1 CH505 Env

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 [auth f]	SCOP2B Superfamily	gp120 core	8103234	3001390	SCOP2B (2022-06-29)
P [auth e]	SCOP2 Family	gp120 core	8102860	4002534	SCOP2 (2022-06-29)
P [auth e]	SCOP2 Superfamily	gp120 core	8102861	3001390	SCOP2 (2022-06-29)
P [auth e]	SCOP2B Superfamily	gp120 core	8103234	3001390	SCOP2B (2022-06-29)
N [auth d]	SCOP2B Superfamily	gp120 core	8103234	3001390	SCOP2B (2022-06-29)
Q [auth c]	SCOP2 Family	Virus ectodomain	8104226	4003841	SCOP2 (2022-06-29)
Q [auth c]	SCOP2 Superfamily	Virus ectodomain	8104227	3001628	SCOP2 (2022-06-29)
Q [auth c]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
O [auth b]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
M [auth a]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	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)
R [auth f]	Omp85	e7lu9f1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
P [auth e]	Omp85	e7lu9e1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
N [auth d]		e7lu9d1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
Q [auth c]	Omp85	e7lu9c1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
O [auth b]	Omp85	e7lu9b1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
M [auth a]		e7lu9a1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
I [auth o]	Omp85	e7lu9o1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
E [auth g]	Omp85	e7lu9g1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
D [auth n]	Omp85	e7lu9n1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
J [auth p]	Omp85	e7lu9p1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
F [auth h]	Omp85	e7lu9h1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
C [auth m]	Omp85	e7lu9m1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
K [auth q]	Omp85	e7lu9q1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
G [auth i]	Omp85	e7lu9i1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
B [auth l]		e7lu9l1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
L [auth r]	Omp85	e7lu9r1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
H [auth j]	Omp85	e7lu9j1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Omp85	ECOD (v295.2)
A [auth k]		e7lu9k1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
N [auth d], P [auth e], R [auth f]	Envelope glycoprotein gp120	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 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
M [auth a], O [auth b], Q [auth c]	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
D [auth n], E [auth g], I [auth o]	DH851.3 light chain	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process peptide antigen assembly with MHC class II protein complex protein-containing complex organization regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class II cellular process MHC protein complex assembly cellular component organization or biogenesis antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen multicellular organismal process regulation of cellular process regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion 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 leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm organelle membrane lysosome MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle
C [auth m], F [auth h], J [auth p]	DH851.3 heavy chain	-	-	cellular anatomical structure extracellular region
B [auth l], G [auth i], K [auth q]	DH851.3 heavy chain	-	-	cellular anatomical structure extracellular region
A [auth k], H [auth j], L [auth r]	DH851.3 light chain	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process peptide antigen assembly with MHC class II protein complex protein-containing complex organization regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class II cellular process MHC protein complex assembly cellular component organization or biogenesis antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen multicellular organismal process regulation of cellular process regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion 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 leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm organelle membrane lysosome MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
N [auth d], P [auth e], R [auth f]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
N [auth d], P [auth e], R [auth f]	IPR036377	Gp120 core superfamily	Homologous Superfamily
N [auth d], P [auth e], R [auth f]	IPR000328	Retroviral envelope protein GP41-like	Domain
N [auth d], P [auth e], R [auth f]	IPR037527	Envelope glycoprotein Gp160	Family
M [auth a], O [auth b], Q [auth c]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
M [auth a], O [auth b], Q [auth c]	IPR036377	Gp120 core superfamily	Homologous Superfamily
M [auth a], O [auth b], Q [auth c]	IPR000328	Retroviral envelope protein GP41-like	Domain
M [auth a], O [auth b], Q [auth c]	IPR037527	Envelope glycoprotein Gp160	Family
D [auth n], E [auth g], I [auth o]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth n], E [auth g], I [auth o]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
D [auth n], E [auth g], I [auth o]	IPR003597	Immunoglobulin C1-set	Domain
D [auth n], E [auth g], I [auth o]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth n], E [auth g], I [auth o]	IPR007110	Immunoglobulin-like domain	Domain
D [auth n], E [auth g], I [auth o]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth m], F [auth h], J [auth p]	IPR003597	Immunoglobulin C1-set	Domain
C [auth m], F [auth h], J [auth p]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth m], F [auth h], J [auth p]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth m], F [auth h], J [auth p]	IPR007110	Immunoglobulin-like domain	Domain
C [auth m], F [auth h], J [auth p]	IPR050380	Immune Recognition and Response Modulators	Family
C [auth m], F [auth h], J [auth p]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B [auth l], G [auth i], K [auth q]	IPR003597	Immunoglobulin C1-set	Domain
B [auth l], G [auth i], K [auth q]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth l], G [auth i], K [auth q]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth l], G [auth i], K [auth q]	IPR007110	Immunoglobulin-like domain	Domain
B [auth l], G [auth i], K [auth q]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth l], G [auth i], K [auth q]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth k], H [auth j], L [auth r]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth k], H [auth j], L [auth r]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A [auth k], H [auth j], L [auth r]	IPR003597	Immunoglobulin C1-set	Domain
A [auth k], H [auth j], L [auth r]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth k], H [auth j], L [auth r]	IPR007110	Immunoglobulin-like domain	Domain
A [auth k], H [auth j], L [auth r]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site