4D9L

Fab structure of anti-HIV-1 gp120 V2 mAb 697


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Functional and immunochemical cross-reactivity of V2-specific monoclonal antibodies from HIV-1-infected individuals.

Gorny, M.K.Pan, R.Williams, C.Wang, X.H.Volsky, B.O'Neal, T.Spurrier, B.Sampson, J.M.Li, L.Seaman, M.S.Kong, X.P.Zolla-Pazner, S.

(2012) Virology 427: 198-207

  • DOI: 10.1016/j.virol.2012.02.003
  • Primary Citation of Related Structures:  
    4D9L

  • PubMed Abstract: 
  • The recent analysis of the first successful RV144 vaccine trial revealed that a high titer of plasma anti-V2 antibodies (Abs) correlated with a decreased risk of HIV-1 infection in vaccine recipients. To understand the mechanism of immune correlates, ...

    The recent analysis of the first successful RV144 vaccine trial revealed that a high titer of plasma anti-V2 antibodies (Abs) correlated with a decreased risk of HIV-1 infection in vaccine recipients. To understand the mechanism of immune correlates, we studied seven anti-V2 monoclonal Abs (mAbs) developed from HIV-1 infected individuals. The V2 mAbs target conserved epitopes, including the binding site for α4β7 integrin, and are broadly cross-reactive with various gp120 proteins. Preferential usage of the VH1-69 gene by V2 mAbs may depend on selection by the same antigenic structure. Six of seven V2 mAbs weakly neutralized four to eight of the 41 pseudoviruses tested and resistance to neutralization was correlated with longer V2 domains. The data suggest the presence of shared, conserved structural elements in the V2 loop, and these can be used in the design of vaccine immunogens inducing broadly reactive Abs with anti-viral activities.


    Organizational Affiliation

    Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. mirek.gorny@med.nyu.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697LMNO215Homo sapiensMutation(s): 0 
Gene Names: IGL@
Find proteins for Q6GMX4 (Homo sapiens)
Explore Q6GMX4 
Go to UniProtKB:  Q6GMX4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697HIJK223Homo sapiensMutation(s): 0 
Gene Names: IGH@
Find proteins for Q6GMX6 (Homo sapiens)
Explore Q6GMX6 
Go to UniProtKB:  Q6GMX6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.322α = 82.12
b = 82.46β = 70.41
c = 93.212γ = 86.27
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-01-11 
  • Released Date: 2012-03-21 
  • Deposition Author(s): Pan, R.M., Kong, X.P.

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy