4JPI | pdb_00004jpi

Crystal structure of a putative VRC01 germline precursor Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.214 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Rational HIV immunogen design to target specific germline B cell receptors.

Jardine, J.Julien, J.P.Menis, S.Ota, T.Kalyuzhniy, O.McGuire, A.Sok, D.Huang, P.S.MacPherson, S.Jones, M.Nieusma, T.Mathison, J.Baker, D.Ward, A.B.Burton, D.R.Stamatatos, L.Nemazee, D.Wilson, I.A.Schief, W.R.

(2013) Science 340: 711-716

  • DOI: https://doi.org/10.1126/science.1234150
  • Primary Citation Related Structures: 
    4JPI, 4JPJ, 4JPK

  • PubMed Abstract: 

    Vaccine development to induce broadly neutralizing antibodies (bNAbs) against HIV-1 is a global health priority. Potent VRC01-class bNAbs against the CD4 binding site of HIV gp120 have been isolated from HIV-1-infected individuals; however, such bNAbs have not been induced by vaccination. Wild-type gp120 proteins lack detectable affinity for predicted germline precursors of VRC01-class bNAbs, making them poor immunogens to prime a VRC01-class response. We employed computation-guided, in vitro screening to engineer a germline-targeting gp120 outer domain immunogen that binds to multiple VRC01-class bNAbs and germline precursors, and elucidated germline binding crystallographically. When multimerized on nanoparticles, this immunogen (eOD-GT6) activates germline and mature VRC01-class B cells. Thus, eOD-GT6 nanoparticles have promise as a vaccine prime. In principle, germline-targeting strategies could be applied to other epitopes and pathogens.


  • Organizational Affiliation
    • Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 99.65 kDa 
  • Atom Count: 6,905 
  • Modeled Residue Count: 849 
  • Deposited Residue Count: 916 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative VRC01 germline Fab heavy chainA [auth H],
C [auth A]
248Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative VRC01 germline Fab light chainB [auth L],
D [auth B]
210Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.214 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.44α = 90
b = 172.44β = 90
c = 92.43γ = 120
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2013-09-18
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary