Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.13 kDa 
• Atom Count: 3390 
• Modelled Residue Count: 380 
• Deposited Residue Count: 402 
• Unique protein chains: 3

6BIX

HLA-DRB1 in complex with citrullinated LL37 peptide

• DOI: 10.2210/pdb6BIX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-11-03 Released: 2018-01-17 
• Deposition Author(s): Ting, Y.T., Scally, S.W., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.212 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

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

• PubMed: 29317506 
• DOI: 10.1074/jbc.RA117.001013
• Primary Citation of Related Structures:  
  6BIV, 6BIX, 6BIZ, 6BIY, 6BIN, 6BIR, 6BIJ, 6BIL


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A	189	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II DR-beta (HLA-DR B)	B	200	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LL37_Cit91	C	13	Homo sapiens	Mutation(s): 0  Gene Names: CAMP, CAP18, FALL39, HSD26
UniProt & NIH Common Fund Data Resources
Find proteins for P49913 (Homo sapiens) Explore P49913  Go to UniProtKB:  P49913
PHAROS:  P49913 GTEx:  ENSG00000164047

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CIR	C	L-PEPTIDE LINKING	C6 H13 N3 O3		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.212 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.337	α = 90
b = 183.059	β = 90
c = 78.435	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-11-03 
• Released Date: 2018-01-17 
Deposition Author(s): Ting, Y.T., Scally, S.W., Rossjohn, J.

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
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary