6FY3

Crystal structure of a V2-directed, RV144 vaccine-like antibody from HIV-1 infection, CAP228-3D, bound to a heterologous V2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Common helical V1V2 conformations of HIV-1 Envelope expose the alpha 4 beta 7 binding site on intact virions.

Wibmer, C.K.Richardson, S.I.Yolitz, J.Cicala, C.Arthos, J.Moore, P.L.Morris, L.

(2018) Nat Commun 9: 4489-4489

  • DOI: https://doi.org/10.1038/s41467-018-06794-x
  • Primary Citation of Related Structures:  
    6FY1, 6FY2, 6FY3

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, 2131, South Africa. c.k.wibmer@gmail.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CAP228-3D Heavy ChainA [auth X],
D [auth H]
238Homo sapiensMutation(s): 0 
Gene Names: IGHV5-51
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CAP228-3D Light ChainB [auth Y],
E [auth L]
218Homo sapiensMutation(s): 0 
Gene Names: IGLV6-57
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CAP45 V2 peptideC [auth Z],
F [auth P]
19Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: Env
UniProt
Find proteins for C6FX86 (Human immunodeficiency virus 1)
Explore C6FX86 
Go to UniProtKB:  C6FX86
Entity Groups  
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UniProt GroupC6FX86
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.36α = 90
b = 43.808β = 93.77
c = 119.91γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesAI104387-01
Poliomyelitis Research FoundationSouth Africa15/83
NHLS Research TrustSouth Africa--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description