2W60 | pdb_00002w60

Anti citrullinated Collagen type 2 antibody acc4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.220 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.169 (Depositor) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2W60

This is version 1.5 of the entry. See complete history

Literature

Structure and pathogenicity of antibodies specific for citrullinated collagen type II in experimental arthritis.

Uysal, H.Bockermann, R.Nandakumar, K.S.Sehnert, B.Bajtner, E.Engstrom, A.Serre, G.Burkhardt, H.Thunnissen, M.M.Holmdahl, R.

(2009) J Exp Medicine 206: 449-462

  • DOI: https://doi.org/10.1084/jem.20081862
  • Primary Citation Related Structures: 
    2W60, 2W65

  • PubMed Abstract: 

    Antibodies to citrulline-modified proteins have a high diagnostic value in rheumatoid arthritis (RA). However, their biological role in disease development is still unclear. To obtain insight into this question, a panel of mouse monoclonal antibodies was generated against a major triple helical collagen type II (CII) epitope (position 359-369; ARGLTGRPGDA) with or without arginines modified by citrullination. These antibodies bind cartilage and synovial tissue, and mediate arthritis in mice. Detection of citrullinated CII from RA patients' synovial fluid demonstrates that cartilage-derived CII is indeed citrullinated in vivo. The structure determination of a Fab fragment of one of these antibodies in complex with a citrullinated peptide showed a surprising beta-turn conformation of the peptide and provided information on citrulline recognition. Based on these findings, we propose that autoimmunity to CII, leading to the production of antibodies specific for both native and citrullinated CII, is an important pathogenic factor in the development of RA.


  • Organizational Affiliation
    • Center for Molecular Protein Science, Biomedical Center I11, Lund University, 221 00 Lund, Sweden.

Macromolecule Content 

  • Total Structure Weight: 47.41 kDa 
  • Atom Count: 3,917 
  • Modeled Residue Count: 435 
  • Deposited Residue Count: 435 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4218Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4217Mus musculusMutation(s): 0 
UniProt
Find proteins for P01837 (Mus musculus)
Explore P01837 
Go to UniProtKB:  P01837
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01837
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NO3

Query on NO3



Download:Ideal Coordinates CCD File
C [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.220 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.169 (Depositor) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.8α = 90
b = 70β = 90
c = 136.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-09
    Changes: Data collection, Database references
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary