Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

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

Macromolecule Content

• Total Structure Weight: 47.25 kDa 
• Atom Count: 3428 
• Residue Count: 381 
• Unique protein chains: 3

4MCZ

Immune Receptor

• DOI: 10.2210/pdb4MCZ/pdb

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


• Deposited: 2013-08-22 Released: 2013-12-04 
• Deposition Author(s): Scally, S.W., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.231 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis.

Scally, S.W., Petersen, J., Law, S.C., Dudek, N.L., Nel, H.J., Loh, K.L., Wijeyewickrema, L.C., Eckle, S.B., van Heemst, J., Pike, R.N., McCluskey, J., Toes, R.E., La Gruta, N.L., Purcell, A.W., Reid, H.H., Thomas, R., Rossjohn, J.

(2013) J Exp Med 210: 2569-2582

• PubMed: 24190431 
• DOI: 10.1084/jem.20131241
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Rheumatoid arthritis (RA) is strongly associated with the human leukocyte antigen (HLA)-DRB1 locus that possesses the shared susceptibility epitope (SE) and the citrullination of self-antigens. We show how citrullinated aggrecan and vimentin epitopes bind to HLA-DRB1*04:01/04. Citrulline was accommodated within the electropositive P4 pocket of HLA-DRB1*04:01/04, whereas the electronegative P4 pocket of the RA-resistant HLA-DRB1*04:02 allomorph interacted with arginine or citrulline-containing epitopes. Peptide elution studies revealed P4 arginine-containing peptides from HLA-DRB1*04:02, but not from HLA-DRB1*04:01/04. Citrullination altered protease susceptibility of vimentin, thereby generating self-epitopes that are presented to T cells in HLA-DRB1*04:01(+) individuals. Using HLA-II tetramers, we observed citrullinated vimentin- and aggrecan-specific CD4(+) T cells in the peripheral blood of HLA-DRB1*04:01(+) RA-affected and healthy individuals. In RA patients, autoreactive T cell numbers correlated with disease activity and were deficient in regulatory T cells relative to healthy individuals. These findings reshape our understanding of the association between citrullination, the HLA-DRB1 locus, and T cell autoreactivity in RA.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.

Macromolecules

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 UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903 GTEx  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DRB1-4 beta chain	B	200	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens) Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS  P01911 GTEx  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Citrullinated Vimentin	C	13	Homo sapiens	Mutation(s): 0  Gene Names: VIM
Find proteins for P08670 (Homo sapiens) Go to UniProtKB:  P08670
NIH Common Fund Data Resources
PHAROS  P08670 GTEx  ENSG00000026025

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	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: 2.41 Å
• R-Value Free: 0.231 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.11	α = 90
b = 183.43	β = 90
c = 77.28	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-22 
• Released Date: 2013-12-04 
Deposition Author(s): Scally, S.W., Rossjohn, J.

Revision History 

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references