6FY0

Crystal structure of a V2-directed, RV144 vaccine-like antibody from HIV-1 infection, CAP228-16H, bound to a heterologous V2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

V2-Directed Vaccine-like Antibodies from HIV-1 Infection Identify an Additional K169-Binding Light Chain Motif with Broad ADCC Activity.

van Eeden, C.Wibmer, C.K.Scheepers, C.Richardson, S.I.Nonyane, M.Lambson, B.Mkhize, N.N.Vijayakumar, B.Sheng, Z.Stanfield-Oakley, S.Bhiman, J.N.Bekker, V.Hermanus, T.Mabvakure, B.Ismail, A.Moody, M.A.Wiehe, K.Garrett, N.Karim, S.A.Dirr, H.Fernandes, M.A.Sayed, Y.Shapiro, L.Ferrari, G.Haynes, B.F.Moore, P.L.Morris, L.

(2018) Cell Rep 25: 3123-3135.e6

  • DOI: https://doi.org/10.1016/j.celrep.2018.11.058
  • Primary Citation of Related Structures:  
    6FY0

  • PubMed Abstract: 

    Antibodies that bind residue K169 in the V2 region of the HIV-1 envelope correlated with reduced risk of infection in the RV144 vaccine trial but were restricted to two ED-motif-encoding light chain genes. Here, we identify an HIV-infected donor with high-titer V2 peptide-binding antibodies and isolate two antibody lineages (CAP228-16H/19F and CAP228-3D) that mediate potent antibody-dependent cell-mediated cytotoxicity (ADCC). Both lineages use the IGHV5-51 heavy chain germline gene, similar to the RV144 antibody CH58, but one lineage (CAP228-16H/19F) uses a light chain without the ED motif. A cocrystal structure of CAP228-16H bound to a V2 peptide identified a IGLV3-21 gene-encoded DDxD motif that is used to bind K169, with a mechanism that allows CAP228-16H to recognize more globally relevant V2 immunotypes. Overall, these data further our understanding of the development of cross-reactive, V2-binding, antiviral antibodies and effectively expand the human light chain repertoire able to respond to RV144-like immunogens.


  • Organizational Affiliation

    National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CAP228-16H Heavy ChainA [auth H],
D [auth I]
235Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CAP228-16H Light ChainB [auth L],
C [auth M]
213Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CAP45 V2 peptideE [auth A],
F [auth P]
19Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for L7TQU8 (Human immunodeficiency virus 1)
Explore L7TQU8 
Go to UniProtKB:  L7TQU8
Entity Groups  
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UniProt GroupL7TQU8
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.299α = 90
b = 104.265β = 90
c = 212.218γ = 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 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description