6FY2

Crystal structure of a V2p-reactive RV144 vaccine-like antibody, CAP228-16H, in complex with a heterologous CAP225 V1V2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1038/s41467-018-06794-x
  • Primary Citation of Related Structures:  
    6FY2, 6FY1, 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 ...

    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 the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4041, South Africa.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAP228-16H Heavy ChainA [auth H], D [auth X]235Homo sapiensMutation(s): 0 
Gene Names: IGHV5-51
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CAP228-16H Light ChainB [auth L], E [auth Y]213Homo sapiensMutation(s): 0 
Gene Names: IGLV3-21
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CAP225 Scaffolded V1V2C [auth P], F [auth Z]137Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: Env
UniProt
Find proteins for A0A3F2YM25 (Human immunodeficiency virus 1)
Explore A0A3F2YM25 
Go to UniProtKB:  A0A3F2YM25
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.354α = 90
b = 41.757β = 96.81
c = 144.524γ = 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