4QHN

I2 (unbound) from CH103 Lineage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains.

Fera, D.Schmidt, A.G.Haynes, B.F.Gao, F.Liao, H.X.Kepler, T.B.Harrison, S.C.

(2014) Proc.Natl.Acad.Sci.USA 111: 10275-10280

  • DOI: 10.1073/pnas.1409954111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rapidly evolving pathogens, such as human immunodeficiency and influenza viruses, escape immune defenses provided by most vaccine-induced antibodies. Proposed strategies to elicit broadly neutralizing antibodies require a deeper understanding of anti ...

    Rapidly evolving pathogens, such as human immunodeficiency and influenza viruses, escape immune defenses provided by most vaccine-induced antibodies. Proposed strategies to elicit broadly neutralizing antibodies require a deeper understanding of antibody affinity maturation and evolution of the immune response to vaccination or infection. In HIV-infected individuals, viruses and B cells evolve together, creating a virus-antibody "arms race." Analysis of samples from an individual designated CH505 has illustrated the interplay between an antibody lineage, CH103, and autologous viruses at various time points. The CH103 antibodies, relatively broad in their neutralization spectrum, interact with the CD4 binding site of gp120, with a contact dominated by CDRH3. We show by analyzing structures of progenitor and intermediate antibodies and by correlating them with measurements of binding to various gp120s that there was a shift in the relative orientation of the light- and heavy-chain variable domains during evolution of the CH103 lineage. We further show that mutations leading to this conformational shift probably occurred in response to insertions in variable loop 5 (V5) of the HIV envelope. The shift displaced the tips of the light chain away from contact with V5, making room for the inserted residues, which had allowed escape from neutralization by the progenitor antibody. These results, which document the selective mechanism underlying this example of a virus-antibody arms race, illustrate the functional significance of affinity maturation by mutation outside the complementarity determining region surface of the antibody molecule.


    Organizational Affiliation

    Laboratory of Molecular Medicine andHoward Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115; harrison@crystal.harvard.edu.,Laboratory of Molecular Medicine and.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710; and.,Department of Microbiology and Immunology, Boston University, Boston, MA 02118.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
I2 heavy chain
A
232Homo sapiensMutation(s): 0 
Gene Names: IGH@
Find proteins for Q6GMX6 (Homo sapiens)
Go to UniProtKB:  Q6GMX6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
I2 light chain
B
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.878α = 90.00
b = 66.955β = 90.00
c = 128.830γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Database references
  • Version 1.2: 2014-07-30
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description