4HK3

I2 Fab (unbound) from CH65-CH67 Lineage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody.

Schmidt, A.G.Xu, H.Khan, A.R.O'Donnell, T.Khurana, S.King, L.R.Manischewitz, J.Golding, H.Suphaphiphat, P.Carfi, A.Settembre, E.C.Dormitzer, P.R.Kepler, T.B.Zhang, R.Moody, M.A.Haynes, B.F.Liao, H.X.Shaw, D.E.Harrison, S.C.

(2013) Proc.Natl.Acad.Sci.USA 110: 264-269

  • DOI: 10.1073/pnas.1218256109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Affinity maturation refines a naive B-cell response by selecting mutations in antibody variable domains that enhance antigen binding. We describe a B-cell lineage expressing broadly neutralizing influenza virus antibodies derived from a subject immun ...

    Affinity maturation refines a naive B-cell response by selecting mutations in antibody variable domains that enhance antigen binding. We describe a B-cell lineage expressing broadly neutralizing influenza virus antibodies derived from a subject immunized with the 2007 trivalent vaccine. The lineage comprises three mature antibodies, the unmutated common ancestor, and a common intermediate. Their heavy-chain complementarity determining region inserts into the conserved receptor-binding pocket of influenza HA. We show by analysis of structures, binding kinetics and long time-scale molecular dynamics simulations that antibody evolution in this lineage has rigidified the initially flexible heavy-chain complementarity determining region by two nearly independent pathways and that this preconfiguration accounts for most of the affinity gain. The results advance our understanding of strategies for developing more broadly effective influenza vaccines.


    Organizational Affiliation

    Laboratory of Molecular Medicine, Children's Hospital, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
I2 heavy chain
J
237N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
I2 light chain
N
214Homo sapiensMutation(s): 0 
Gene Names: IGL@
Find proteins for Q8N355 (Homo sapiens)
Go to UniProtKB:  Q8N355
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.221 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 102.455α = 90.00
b = 102.455β = 90.00
c = 81.492γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2012-12-05
    Type: Database references
  • Version 1.2: 2013-01-16
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description