5T3X

3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074.


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth B]SCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
B [auth G]SCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth B]GP41_1ste5t3xB1 A: a+b duplicates or obligate multimersX: MPER trimer (From Topology)H: MPER trimer (From Topology)T: MPER trimerF: GP41_1stECOD (1.6)
B [auth G]GP120_2nde5t3xG3 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: GP120_2ndECOD (1.6)
B [auth G]GP120_3rde5t3xG1 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: GP120_3rdECOD (1.6)
B [auth G]GP120_1ste5t3xG2 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)
C [auth H]V-set_8e5t3xH2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
C [auth H]C1-set_1e5t3xH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
D [auth L]C1-sete5t3xL2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-setECOD (1.6)
D [auth L]V-set_3e5t3xL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
E [auth D]V-set_8e5t3xD1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
E [auth D]C1-set_1e5t3xD2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
F [auth E]C1-sete5t3xE1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-setECOD (1.6)
F [auth E]V-set_3e5t3xE2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
C [auth H]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
D [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
E [auth D]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
F [auth E]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
C [auth H]Fv 10-1074 VH Homo sapiens (human) IGHV4-59*01, IGHV4-59*02, IGHV4-59*08, IGHV4-4*08 V-DOMAIN VH IG FV-HEAVY_LAMBDA IMGT (202447-0)
D [auth L]Fv 10-1074 L-LAMBDA Homo sapiens (human) IGLV3-21*01, IGLJ2*01, IGLJ7*01, IGLJ3*01, IGLC2*01, IGLC2*02, IGLC3*04 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FV-HEAVY_LAMBDA IMGT (202447-0)
E [auth D]Fab IOMA VH-CH1 Homo sapiens (human) IGHV1-2*02, IGHJ1*01, IGHJ4*01, IGHJ5*02, IGHJ4*02, IGHJ4*03, IGHG1*03 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_LAMBDA IMGT (202447-0)
F [auth E]Fab IOMA L-LAMBDA Homo sapiens (human) IGLV2-23*01, IGLJ3*02, IGLC2*01, IGLC2*02, IGLC3*04 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-1_LAMBDA IMGT (202447-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
C [auth H]Heavy ChainIGHV4 -envelope glycoprotein gp160SAbDab (2024-11-29)
E [auth D]Heavy ChainIGHV1 -envelope glycoprotein gp160SAbDab (2024-11-29)
F [auth E]Light ChainIGLV2 Lambdaenvelope glycoprotein gp160SAbDab (2024-11-29)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

ChainNameTargetProvenance Source
C [auth H] Zinlirvimab HIV-1 gp120 V3Therapeutic SAbDab (2024-11-29)
D [auth L] Zinlirvimab HIV-1 gp120 V3Therapeutic SAbDab (2024-11-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth B]PF00517Retroviral envelope protein (GP41)Retroviral envelope protein- Family
B [auth G]PF00516Envelope glycoprotein GP120 (GP120)Envelope glycoprotein GP120- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth B]Envelope glycoprotein gp160
B [auth G]Envelope glycoprotein gp160
C [auth H]10-1074 Heavy Chain---
D [auth L]10-1074 Light Chain---
E [auth D]IOMA Heavy Chain---
F [auth E]IOMA Light Chain---