4HPO

Crystal structure of RV144-elicited antibody CH58 in complex with V2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 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
CH58 Fab heavy chainA [auth H]231Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CH58 Fab light chainB [auth L]216Homo sapiensMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
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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
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UniProt GroupG9HS63
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.594α = 90
b = 75.804β = 111.99
c = 54.688γ = 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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary