4BKL

Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Epitope-Specific Antibody Response is Controlled by Immunoglobulin Vh Polymorphisms.

Raposo, B.Dobritzsch, D.Ge, C.Ekman, D.Xu, B.Lindh, I.Forster, M.Uysal, H.Nandakumar, K.S.Schneider, G.Holmdahl, R.

(2014) J.Exp.Med. 211: 405

  • DOI: 10.1084/jem.20130968

  • PubMed Abstract: 
  • Autoantibody formation is essential for the development of certain autoimmune diseases like rheumatoid arthritis (RA). Anti-type II collagen (CII) antibodies are found in RA patients; they interact with cartilage in vivo and are often highly pathogen ...

    Autoantibody formation is essential for the development of certain autoimmune diseases like rheumatoid arthritis (RA). Anti-type II collagen (CII) antibodies are found in RA patients; they interact with cartilage in vivo and are often highly pathogenic in the mouse. Autoreactivity to CII is directed to multiple epitopes and conserved between mice and humans. We have previously mapped the antibody response to CII in a heterogeneous stock cohort of mice, with a strong association with the IgH locus. We positioned the genetic polymorphisms and determined the structural requirements controlling antibody recognition of one of the major CII epitopes. Polymorphisms at positions S31R and W33T of the associated variable heavy chain (VH) allele were identified and confirmed by gene sequencing. The Fab fragment binding the J1 epitope was crystallized, and site-directed mutagenesis confirmed the importance of those two variants for antigen recognition. Back mutation to germline sequence provided evidence for a preexisting recognition of the J1 epitope. These data demonstrate a genetic association of epitope-specific antibody responses with specific VH alleles, and it highlights the importance of germline-encoded antibodies in the pathogenesis of antibody-mediated autoimmune diseases.


    Organizational Affiliation

    Section for Medical Inflammation Research and 2 Section for Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M2139 FAB FRAGMENT HEAVY CHAIN
A
231N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
M2139 FAB FRAGMENT LIGHT CHAIN
B
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
J1 EPITOPE
E, F, G
37Mus musculusMutation(s): 0 
Gene Names: Col2a1
Find proteins for P28481 (Mus musculus)
Go to UniProtKB:  P28481
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
E, F, G
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.180α = 90.00
b = 95.180β = 90.00
c = 190.420γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-03-05
    Type: Database references
  • Version 1.2: 2014-03-26
    Type: Database references