3G9R

Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e3g9rA1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e3g9rB1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e3g9rC1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e3g9rD1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e3g9rE1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e3g9rF1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.5.490	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
B	1.20.5.490	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
C	1.20.5.490	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
D	1.20.5.490	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
E	1.20.5.490	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
F	1.20.5.490	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00517	Retroviral envelope protein (GP41)	Retroviral envelope protein	-	Family
A, B, C, D, E A, B, C, D, E, F	PF07716	Basic region leucine zipper (bZIP_2)	Basic region leucine zipper	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4	TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding transcription regulator activity DNA-binding transcription factor activity mediator complex binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding structural molecule activity	response to nutrient levels response to stimulus response to stress response to amino acid starvation response to starvation positive regulation of cellular response to amino acid starvation cellular response to stimulus regulation of response to nutrient levels regulation of cellular process positive regulation of biological process regulation of cellular response to stress cellular response to amino acid starvation positive regulation of response to stimulus cellular response to stress response to nutrient levels response to stimulus response to stress response to amino acid starvation response to starvation positive regulation of cellular response to amino acid starvation cellular response to stimulus regulation of response to nutrient levels regulation of cellular process positive regulation of biological process regulation of cellular response to stress cellular response to amino acid starvation positive regulation of response to stimulus cellular response to stress regulation of response to stress positive regulation of cellular process regulation of biological process biological regulation cellular response to starvation cellular response to nutrient levels regulation of response to stimulus cellular process regulation of cellular response to amino acid starvation positive regulation of response to nutrient levels transcription preinitiation complex assembly positive regulation of macromolecule biosynthetic process regulation of primary metabolic process cellular component biogenesis nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process cellular component assembly transcription by RNA polymerase II organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process RNA polymerase II preinitiation complex assembly metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of RNA polymerase II transcription preinitiation complex assembly regulation of cellular component organization positive regulation of cellular component organization cellular biosynthetic process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular metabolic process cellular component organization protein-DNA complex organization RNA biosynthetic process nucleic acid biosynthetic process regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly organic substance metabolic process positive regulation of biosynthetic process protein-containing complex assembly cellular component organization or biogenesis regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of RNA polymerase II transcription preinitiation complex assembly protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of transcription initiation by RNA polymerase II protein-DNA complex assembly regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II positive regulation of cellular biosynthetic process protein localization localization cellular localization protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to nuclear periphery protein localization to nucleus amino acid biosynthetic process amino acid metabolic process cellular response to nitrogen compound response to organic substance nitrogen catabolite regulation of transcription regulation of nitrogen utilization intracellular nitrogen homeostasis nitrogen catabolite activation of transcription from RNA polymerase II promoter response to organonitrogen compound response to nitrogen compound cellular response to organonitrogen compound chemical homeostasis response to chemical homeostatic process cellular response to endogenous stimulus nitrogen catabolite activation of transcription intracellular chemical homeostasis cellular response to organic substance nitrogen catabolite regulation of transcription from RNA polymerase II promoter response to endogenous stimulus response to nutrient nitrogen utilization cellular response to chemical stimulus cellular homeostasis cellular response to nutrient signaling signal transduction intracellular signal transduction cell communication negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process regulation of ribosomal protein gene transcription by RNA polymerase II negative regulation of ribosomal protein gene transcription by RNA polymerase II viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization membrane fusion fusion of virus membrane with host plasma membrane regulation of establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of leukocyte activation establishment of T cell polarity 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 T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation 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 regulation of localization regulation of protein localization positive regulation of receptor clustering positive regulation of protein localization to membrane localization within membrane protein localization to membrane regulation of cellular 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 response to host defenses response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response response to biotic stimulus modulation by symbiont of host process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process plasma membrane raft distribution 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 viral gene expression viral protein processing	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle membrane virion component virion membrane RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle membrane 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 host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR004827	Basic-leucine zipper domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR046347	Basic-leucine zipper domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036377	Gp120 core superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000328	Retroviral envelope protein GP41-like	Domain
A, B, C, D, E A, B, C, D, E, F	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 R01GM133198.