Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47133.28 
• Atom Count: 3134 
• 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


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.212 
• R-Value Work: 0.169 

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:  
  6BIZ, 6BIY, 6BIV, 6BIR, 6BIN, 6BIL, 6BIJ


• 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 polarisation 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 b-chain polymorphisms that resided outside the SE motif and were consistent with sequences of naturally presented peptide ligands. Structure determination of eight HLA-DR4-self-epitope complexes revealed strict conformational convergence of the P4-Cit and surrounding HLA b-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: 

Monash University, Australia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR alpha chain	A	189	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
HLA class II DR-beta (HLA-DR B)	B	200	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P13760 (Homo sapiens) Go to Gene View: HLA-DRB1 Go to UniProtKB:  P13760

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
LL37_Cit91	C	13	Homo sapiens	Mutation(s): 0  Gene Names: CAMP (CAP18, FALL39)
Find proteins for P49913 (Homo sapiens) Go to Gene View: CAMP Go to UniProtKB:  P49913

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A	N-ACETYL-D-GLUCOSAMINE 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: 2.2 Å
• R-Value Free: 0.212 
• R-Value Work: 0.169 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 67.337	α = 90.00
b = 183.059	β = 90.00
c = 78.435	γ = 90.00

Software Package:

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

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
  Type: Database references, Structure summary
• Version 1.2: 2018-03-14
  Type: Database references