6DE7

Crystal Structure at 4.3 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Interdomain Stabilization 113C-429GCG in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth B]SCOP2 FamilyVirus ectodomain8085601 4003841 SCOP2 (2022-06-29)
A [auth B]SCOP2 SuperfamilyVirus ectodomain8085602 3001628 SCOP2 (2022-06-29)
D [auth G]SCOP2B Superfamilygp120 core8080371 3001390 SCOP2B (2022-06-29)
E [auth H]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like8091519 3000071 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth B]PF00517e6de7B1 A: a+b duplicates or obligate multimersX: MPER trimer (From Topology)H: MPER trimer (From Topology)T: MPER trimerF: PF00517ECOD (1.6)
B [auth D]PF07654e6de7D2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
B [auth D]PF07686e6de7D1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
C [auth E]PF07654e6de7E1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
C [auth E]PF07686e6de7E2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
D [auth G]PF00516e6de7G2 A: beta barrelsX: V1/V2 domain in HIV gp120 (From Topology)H: V1/V2 domain in HIV gp120 (From Topology)T: V1/V2 domain in HIV gp120F: PF00516ECOD (1.6)
D [auth G]PF00516e6de7G1 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: PF00516ECOD (1.6)
D [auth G]PF00516e6de7G3 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: PF00516ECOD (1.6)
E [auth H]PF07654e6de7H2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
E [auth H]PF07686e6de7H1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
F [auth L]PF07654e6de7L1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
F [auth L]PF07686e6de7L2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
B [auth D]Fab 35O22, broadly neutralizing antibody VH-CH1 Homo sapiens (human) IGHV1-18*01, IGHV1-18*04, IGHJ1*01, IGHJ4*01, IGHJ5*02, IGHJ4*02, IGHJ4*03, IGHG1*03 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_LAMBDA IMGT (202416-0)
C [auth E]Fab 35O22, broadly neutralizing antibody L-LAMBDA Homo sapiens (human) IGLV2-14*02, IGLV2-18*02, IGLV2-23*01, IGLV2-23*02, IGLV2-23*03, IGLJ1*01, IGLC2*01, IGLC2*02, IGLC3*04 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-1_LAMBDA IMGT (202416-0)
E [auth H]Fab PGT122, broadly neutralizing antibody VH-CH1 Homo sapiens (human) IGHV4-59*02, IGHJ3*01, IGHG1*03 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_LAMBDA IMGT (202416-0)
F [auth L]Fab PGT122, broadly neutralizing antibody L-LAMBDA Homo sapiens (human) IGLV3-21*01, IGLV3-21*02, IGLJ3*02, IGLC3*03 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-1_LAMBDA IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
E [auth H]Heavy ChainIGHV4 -envelope glycoprotein gp160SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth B]PF00517Retroviral envelope protein (GP41)Retroviral envelope protein- Family
B [auth D]PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
D [auth G]PF00516Envelope glycoprotein GP120 (GP120)Envelope glycoprotein GP120- Family
E [auth H]PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
F [auth L]PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth B]Envelope glycoprotein gp160
B [auth D]35O22 heavy chain
C [auth E]35O22 light chain---
D [auth G]Envelope glycoprotein gp160
E [auth H]PGT122 Heavy chain
F [auth L]PGT122 Light Chain

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth B]IPR000777Human immunodeficiency virus 1, envelope glycoprotein Gp120Domain
A [auth B]IPR036377Gp120 core superfamilyHomologous Superfamily
A [auth B]IPR000328Retroviral envelope protein GP41-likeDomain
A [auth B]IPR037527Envelope glycoprotein Gp160Family
B [auth D]IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
B [auth D]IPR003597Immunoglobulin C1-setDomain
B [auth D]IPR013783Immunoglobulin-like foldHomologous Superfamily
B [auth D]IPR007110Immunoglobulin-like domainDomain
B [auth D]IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
D [auth G]IPR000777Human immunodeficiency virus 1, envelope glycoprotein Gp120Domain
D [auth G]IPR036377Gp120 core superfamilyHomologous Superfamily
D [auth G]IPR000328Retroviral envelope protein GP41-likeDomain
D [auth G]IPR037527Envelope glycoprotein Gp160Family
E [auth H]IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
E [auth H]IPR003597Immunoglobulin C1-setDomain
E [auth H]IPR013783Immunoglobulin-like foldHomologous Superfamily
E [auth H]IPR007110Immunoglobulin-like domainDomain
E [auth H]IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
F [auth L]IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
F [auth L]IPR003597Immunoglobulin C1-setDomain
F [auth L]IPR013783Immunoglobulin-like foldHomologous Superfamily
F [auth L]IPR007110Immunoglobulin-like domainDomain
F [auth L]IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site

Pharos: Disease Associations Pharos Homepage Annotation