4RIS

Structural Analysis of the Unmutated Ancestor of the HIV-1 Envelope V2 Region Antibody CH58 Isolated From an RV144 HIV-1 Vaccine Efficacy Trial Vaccinee and Associated with Decreased Transmission Risk


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.170 

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This is version 1.1 of the entry. See complete history


Literature

Structural analysis of the unmutated ancestor of the HIV-1 envelope V2 region antibody CH58 isolated from an RV144 vaccine efficacy trial vaccinee.

Nicely, N.I.Wiehe, K.Kepler, T.B.Jaeger, F.H.Dennison, S.M.Rerks-Ngarm, S.Nitayaphan, S.Pitisuttithum, P.Kaewkungwal, J.Robb, M.L.O'Connell, R.J.Michael, N.L.Kim, J.H.Liao, H.X.Munir Alam, S.Hwang, K.K.Bonsignori, M.Haynes, B.F.

(2015) EBioMedicine 2: 713-722

  • DOI: https://doi.org/10.1016/j.ebiom.2015.06.016
  • Primary Citation of Related Structures:  
    4RIR, 4RIS

  • PubMed Abstract: 

    Human monoclonal antibody CH58 isolated from an RV144 vaccinee binds at Lys169 of the HIV-1 Env gp120 V2 region, a site of vaccine-induced immune pressure. CH58 neutralizes HIV-1 CRF_01 AE strain 92TH023 and mediates ADCC against CD4 + T cell targets infected with CRF_01 AE tier 2 virus. CH58 and other antibodies that bind to a gp120 V2 epitope have a second light chain complementarity determining region (LCDR2) bearing a glutamic acid, aspartic acid (ED) motif involved in forming salt bridges with polar, basic side amino acid side chains in V2. In an effort to learn how V2 responses develop, we determined the crystal structures of the CH58-UA antibody unliganded and bound to V2 peptide. The structures showed an LCDR2 structurally pre-conformed from germline to interact with V2 residue Lys169. LCDR3 was subject to conformational selection through the affinity maturation process. Kinetic analyses demonstrate that only a few contacts were responsible for a 2000-fold increase in KD through maturation, and this effect was predominantly due to an improvement in off-rate. This study shows that preconformation and preconfiguration can work in concert to produce antibodies with desired immunogenic properties.


  • Organizational Affiliation

    Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinA [auth P]18Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q70966 (Human immunodeficiency virus 1)
Explore Q70966 
Go to UniProtKB:  Q70966
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70966
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CH58-UA Fab heavy chainB [auth H]231Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CH58-UA Fab light chainC [auth L]216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.719α = 90
b = 53.908β = 108.92
c = 73.573γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references