6ATZ

HLA-DRB1*1402 in complex with citrullinated fibrinogen peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 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

    The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A, C
177Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
Find proteins for P01903 (Homo sapiens)
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II antigen
B, D
188Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for A0A0A1I7H6 (Homo sapiens)
Go to UniProtKB:  A0A0A1I7H6
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen beta chain
E, F
12Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
Go to UniProtKB:  P02675
NIH Common Fund Data Resources
PHAROS  P02675
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download CCD File 
B
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.881α = 90
b = 72.885β = 107.4
c = 95.316γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references