4HPY

Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2.

Liao, H.X.Bonsignori, M.Alam, S.M.McLellan, J.S.Tomaras, G.D.Moody, M.A.Kozink, D.M.Hwang, K.K.Chen, X.Tsao, C.Y.Liu, P.Lu, X.Parks, R.J.Montefiori, D.C.Ferrari, G.Pollara, J.Rao, M.Peachman, K.K.Santra, S.Letvin, N.L.Karasavvas, N.Yang, Z.Y.Dai, K.Pancera, M.Gorman, J.Wiehe, K.Nicely, N.I.Rerks-Ngarm, S.Nitayaphan, S.Kaewkungwal, J.Pitisuttithum, P.Tartaglia, J.Sinangil, F.Kim, J.H.Michael, N.L.Kepler, T.B.Kwong, P.D.Mascola, J.R.Nabel, G.J.Pinter, A.Zolla-Pazner, S.Haynes, B.F.

(2013) Immunity 38: 176-186

  • DOI: https://doi.org/10.1016/j.immuni.2012.11.011
  • Primary Citation of Related Structures:  
    4HPO, 4HPY, 4HQQ

  • PubMed Abstract: 

    The RV144 HIV-1 trial of the canary pox vector (ALVAC-HIV) plus the gp120 AIDSVAX B/E vaccine demonstrated an estimated efficacy of 31%, which correlated directly with antibodies to HIV-1 envelope variable regions 1 and 2 (V1-V2). Genetic analysis of trial viruses revealed increased vaccine efficacy against viruses matching the vaccine strain at V2 residue 169. Here, we isolated four V2 monoclonal antibodies from RV144 vaccinees that recognize residue 169, neutralize laboratory-adapted HIV-1, and mediate killing of field-isolate HIV-1-infected CD4(+) T cells. Crystal structures of two of the V2 antibodies demonstrated that residue 169 can exist within divergent helical and loop conformations, which contrasted dramatically with the β strand conformation previously observed with a broadly neutralizing antibody PG9. Thus, RV144 vaccine-induced immune pressure appears to target a region that may be both sequence variable and structurally polymorphic. Variation may signal sites of HIV-1 envelope vulnerability, providing vaccine designers with new options.


  • Organizational Affiliation

    Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA. hliao@duke.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CH59 Fab heavy chainA [auth H]225Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6N089 (Homo sapiens)
Explore Q6N089 
Go to UniProtKB:  Q6N089
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N089
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CH59 Fab light chainB [auth L]215Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8N5F4 (Homo sapiens)
Explore Q8N5F4 
Go to UniProtKB:  Q8N5F4
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UniProt GroupQ8N5F4
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160C [auth P]19Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for G9HS63 (Human immunodeficiency virus 1)
Explore G9HS63 
Go to UniProtKB:  G9HS63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9HS63
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.888α = 90
b = 79.15β = 90
c = 127.112γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary