6BIY

HLA-DRB1 in complex with Histone 2B peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis.

Ting, Y.T.Petersen, J.Ramarathinam, S.H.Scally, S.W.Loh, K.L.Thomas, R.Suri, A.Baker, D.G.Purcell, A.W.Reid, H.H.Rossjohn, J.

(2018) J Biol Chem 293: 3236-3251

  • DOI: 10.1074/jbc.RA117.001013
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The HLA-DRB1 locus is strongly associated with rheumatoid arthritis (RA) susceptibility, whereupon citrullinated self-peptides bind to HLA-DR molecules bearing the shared epitope (SE) amino acid motif. However, the differing propensity for c ...

    The HLA-DRB1 locus is strongly associated with rheumatoid arthritis (RA) susceptibility, whereupon citrullinated self-peptides bind to HLA-DR molecules bearing the shared epitope (SE) amino acid motif. However, the differing propensity for citrullinated/non-citrullinated self-peptides to bind given HLA-DR allomorphs remains unclear. Here, we used a fluorescence polarization assay to determine a hierarchy of binding affinities of 34 self-peptides implicated in RA against three HLA-DRB1 allomorphs (HLA-DRB1*04:01/*04:04/*04:05) each possessing the SE motif. For all three HLA-DRB1 allomorphs, we observed a strong correlation between binding affinity and citrullination at P4 of the bound peptide ligand. A differing hierarchy of peptide-binding affinities across the three HLA-DRB1 allomorphs was attributable to the β-chain polymorphisms that resided outside the SE motif and were consistent with sequences of naturally presented peptide ligands. Structural determination of eight HLA-DR4-self-epitope complexes revealed strict conformational convergence of the P4-Cit and surrounding HLA β-chain residues. Polymorphic residues that form part of the P1 and P9 pockets of the HLA-DR molecules provided a structural basis for the preferential binding of the citrullinated self-peptides to the HLA-DR4 allomorphs. Collectively, we provide a molecular basis for the interplay between citrullination of self-antigens and HLA polymorphisms that shape peptide-HLA-DR4 binding affinities in RA.


    Organizational Affiliation

    the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone2B_69-81
C
13Homo sapiensMutation(s): 0 
Gene Names: H2BC1HIST1H2BATSH2B
Find proteins for Q96A08 (Homo sapiens)
Go to UniProtKB:  Q96A08
NIH Common Fund Data Resources
PHAROS  Q96A08

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
189Homo 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II DR-beta (HLA-DR B)
B
200Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS  P01911
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
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.826α = 90
b = 182.478β = 90
c = 76.807γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references, Structure summary
  • Version 1.2: 2018-03-14
    Changes: Database references