6FY3 image
Deposition Date 2018-03-10
Release Date 2018-09-05
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6FY3
Keywords:
Title:
Crystal structure of a V2-directed, RV144 vaccine-like antibody from HIV-1 infection, CAP228-3D, bound to a heterologous V2 peptide
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.60 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:CAP228-3D Heavy Chain
Chain IDs:A (auth: X), D (auth: H)
Chain Length:238
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:CAP228-3D Light Chain
Chain IDs:B (auth: Y), E (auth: L)
Chain Length:218
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CAP45 V2 peptide
Chain IDs:C (auth: Z), F (auth: P)
Chain Length:19
Number of Molecules:2
Biological Source:Human immunodeficiency virus 1
Primary Citation
Common helical V1V2 conformations of HIV-1 Envelope expose the alpha 4 beta 7 binding site on intact virions.
Nat Commun 9 4489 4489 (2018)
PMID: 30367034 DOI: 10.1038/s41467-018-06794-x

Abstact

The α4β7 integrin is a non-essential HIV-1 adhesion receptor, bound by the gp120 V1V2 domain, facilitating rapid viral dissemination into gut-associated lymphoid tissues. Antibodies blocking this interaction early in infection can improve disease outcome, and V1V2-targeted antibodies were correlated with moderate efficacy reported from the RV144 HIV-1 vaccine trial. Monoclonal α4β7-blocking antibodies recognise two slightly different helical V2 conformations, and current structural data suggests their binding sites are occluded in prefusion envelope trimers. Here, we report cocrystal structures of two α4β7-blocking antibodies from an infected donor complexed with scaffolded V1V2 or V2 peptides. Both antibodies recognised the same helix-coil V2 conformation as RV144 antibody CH58, identifying a frequently sampled alternative conformation of full-length V1V2. In the context of Envelope, this α-helical form of V1V2 displays highly exposed α4β7-binding sites, potentially providing a functional role for non-native Envelope on virion or infected cell surfaces in HIV-1 dissemination, pathogenesis, and vaccine design.

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Primary Citation of related structures