4Q2Z

Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

HIV-1 Receptor Binding Site-Directed Antibodies Using a VH1-2 Gene Segment Orthologue Are Activated by Env Trimer Immunization.

Navis, M.Tran, K.Bale, S.Phad, G.E.Guenaga, J.Wilson, R.Soldemo, M.McKee, K.Sundling, C.Mascola, J.Li, Y.Wyatt, R.T.Karlsson Hedestam, G.B.

(2014) Plos Pathog. 10: e1004337-e1004337

  • DOI: 10.1371/journal.ppat.1004337

  • PubMed Abstract: 
  • Broadly neutralizing antibodies (bNAbs) isolated from chronically HIV-1 infected individuals reveal important information regarding how antibodies target conserved determinants of the envelope glycoprotein (Env) spike such as the primary receptor CD4 ...

    Broadly neutralizing antibodies (bNAbs) isolated from chronically HIV-1 infected individuals reveal important information regarding how antibodies target conserved determinants of the envelope glycoprotein (Env) spike such as the primary receptor CD4 binding site (CD4bs). Many CD4bs-directed bNAbs use the same heavy (H) chain variable (V) gene segment, VH1-2*02, suggesting that activation of B cells expressing this allele is linked to the generation of this type of Ab. Here, we identify the rhesus macaque VH1.23 gene segment to be the closest macaque orthologue to the human VH1-2 gene segment, with 92% homology to VH1-2*02. Of the three amino acids in the VH1-2*02 gene segment that define a motif for VRC01-like antibodies (W50, N58, flanking the HCDR2 region, and R71), the two identified macaque VH1.23 alleles described here encode two. We demonstrate that immunization with soluble Env trimers induced CD4bs-specific VH1.23-using Abs with restricted neutralization breadth. Through alanine scanning and structural studies of one such monoclonal Ab (MAb), GE356, we demonstrate that all three HCDRs are involved in neutralization. This contrasts to the highly potent CD4bs-directed VRC01 class of bNAb, which bind Env predominantly through the HCDR2. Also unlike VRC01, GE356 was minimally modified by somatic hypermutation, its light (L) chain CDRs were of average lengths and it displayed a binding footprint proximal to the trimer axis. These results illustrate that the Env trimer immunogen used here activates B cells encoding a VH1-2 gene segment orthologue, but that the resulting Abs interact distinctly differently with the HIV-1 Env spike compared to VRC01.


    Organizational Affiliation

    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America.,IAVI Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, California, United States of America; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.,IAVI Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, California, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
H, A
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
L, B
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 48.243α = 92.39
b = 67.909β = 94.13
c = 69.980γ = 109.69
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
HKL-2000data scaling
PHENIXrefinement
PHENIXmodel building
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release