5F6J

Crystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rhesus Macaque in Complex with HIV-1 gp120 Core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.63 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site.

Bradley, T.Fera, D.Bhiman, J.Eslamizar, L.Lu, X.Anasti, K.Zhang, R.Sutherland, L.L.Scearce, R.M.Bowman, C.M.Stolarchuk, C.Lloyd, K.E.Parks, R.Eaton, A.Foulger, A.Nie, X.Karim, S.S.Barnett, S.Kelsoe, G.Kepler, T.B.Alam, S.M.Montefiori, D.C.Moody, M.A.Liao, H.X.Morris, L.Santra, S.Harrison, S.C.Haynes, B.F.

(2016) Cell Rep 14: 43-54

  • DOI: https://doi.org/10.1016/j.celrep.2015.12.017
  • Primary Citation of Related Structures:  
    5F6H, 5F6I, 5F6J

  • PubMed Abstract: 

    Antibodies that neutralize autologous transmitted/founder (TF) HIV occur in most HIV-infected individuals and can evolve to neutralization breadth. Autologous neutralizing antibodies (nAbs) against neutralization-resistant (Tier-2) viruses are rarely induced by vaccination. Whereas broadly neutralizing antibody (bnAb)-HIV-Envelope structures have been defined, the structures of autologous nAbs have not. Here, we show that immunization with TF mutant Envs gp140 oligomers induced high-titer, V5-dependent plasma neutralization for a Tier-2 autologous TF evolved mutant virus. Structural analysis of autologous nAb DH427 revealed binding to V5, demonstrating the source of narrow nAb specificity and explaining the failure to acquire breadth. Thus, oligomeric TF Envs can elicit autologous nAbs to Tier-2 HIVs, but induction of bnAbs will require targeting of precursors of B cell lineages that can mature to heterologous neutralization.


  • Organizational Affiliation

    Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: todd.bradley@duke.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade CA [auth G],
B [auth E]
352Human immunodeficiency virus 1Mutation(s): 3 
UniProt
Find proteins for R4GRV3 (Human immunodeficiency virus 1)
Explore R4GRV3 
Go to UniProtKB:  R4GRV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4GRV3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH427 Antibody Light ChainC [auth A],
E [auth F]
216Macaca mulattaMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DH427 Antibody Heavy ChainD [auth B],
F [auth H]
228Macaca mulattaMutation(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: 6.63 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.902α = 90
b = 162.902β = 90
c = 229.854γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-01-20
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Source and taxonomy
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description