6U6O

Crystal structure of a vaccine-elicited anti-HIV-1 rhesus macaque antibody DH846


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates.

Cai, F.Chen, W.H.Wu, W.Jones, J.A.Choe, M.Gohain, N.Shen, X.LaBranche, C.Eaton, A.Sutherland, L.Lee, E.M.Hernandez, G.E.Wu, N.R.Scearce, R.Seaman, M.S.Moody, M.A.Santra, S.Wiehe, K.Tomaras, G.D.Wagh, K.Korber, B.Bonsignori, M.Montefiori, D.C.Haynes, B.F.de Val, N.Joyce, M.G.Saunders, K.O.

(2021) PLoS Pathog 17: e1009624-e1009624

  • DOI: https://doi.org/10.1371/journal.ppat.1009624
  • Primary Citation of Related Structures:  
    6U6M, 6U6O

  • PubMed Abstract: 

    A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.


  • Organizational Affiliation

    Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DH846 Fab heavy chainA [auth H]228Macaca mulattaMutation(s): 0 
Entity Groups  
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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH846 Fab light chainB [auth L]213Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.018α = 90
b = 36.991β = 111.96
c = 87.921γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH-07-2-0067

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary