6ATI

HLA-DRB1*1402 in complex with Vimentin-64Cit59-71


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis.

Scally, S.W.Law, S.C.Ting, Y.T.Heemst, J.V.Sokolove, J.Deutsch, A.J.Bridie Clemens, E.Moustakas, A.K.Papadopoulos, G.K.Woude, D.V.Smolik, I.Hitchon, C.A.Robinson, D.B.Ferucci, E.D.Bernstein, C.N.Meng, X.Anaparti, V.Huizinga, T.Kedzierska, K.Reid, H.H.Raychaudhuri, S.Toes, R.E.Rossjohn, J.El-Gabalawy, H.Thomas, R.

(2017) Ann. Rheum. Dis. 76: 1915-1923

  • DOI: 10.1136/annrheumdis-2017-211300
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The pathogenetic mechanisms by which <i>HLA-DRB1 </i> alleles are associated with anticitrullinated peptide antibody (ACPA)-positive rheumatoid arthritis (RA) are incompletely understood. RA high-risk <i>HLA-DRB1 </i> alleles are known to share a c ...

    The pathogenetic mechanisms by which HLA-DRB1 alleles are associated with anticitrullinated peptide antibody (ACPA)-positive rheumatoid arthritis (RA) are incompletely understood. RA high-risk HLA-DRB1 alleles are known to share a common motif, the 'shared susceptibility epitope (SE)'. Here, the electropositive P4 pocket of HLA-DRB1 accommodates self-peptide residues containing citrulline but not arginine. HLA-DRB1 His/Phe13β stratifies with ACPA-positive RA, while His13βSer polymorphisms stratify with ACPA-negative RA and RA protection. Indigenous North American (INA) populations have high risk of early-onset ACPA-positive RA, whereby HLA-DRB1*04:04 and HLA-DRB1*14:02 are implicated as risk factors for RA in INA. However, HLA-DRB1*14:02 has a His13βSer polymorphism. Therefore, we aimed to verify this association and determine its molecular mechanism.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute Monash University, Clayton, Australia.,Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA.,Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.,Division of Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, Alaska, USA.,Arthritis Centre, University of Manitoba, Winnipeg, Manitoba, Canada.,Faculty of Agricultural Technology, Technological Educational Institute of Ionian Islands, Argostoli Kefalonia, Greece.,Center for Data Sciences, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Department of Medicine/Immunology and Rheumatology, Stanford University, VA Palo Alto Health Care System, Palo Alto, California.,Laboratory of Biochemistry and Biophysics, Faculty of Agricultural Technology, Epirus Institute of Technology, Arta, Greece.,The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Australia.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A, D
189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II antigen
B, E
200N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vimentin-64Cit59-71
C, F
13Homo sapiensMutation(s): 0 
Gene Names: VIM
Find proteins for P08670 (Homo sapiens)
Go to Gene View: VIM
Go to UniProtKB:  P08670
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CIR
Query on CIR
C, F
L-PEPTIDE LINKINGC6 H13 N3 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.270α = 90.00
b = 76.870β = 109.68
c = 94.910γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references