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)

Macromolecule Content

• Total Structure Weight: 47.25 kDa 
• Atom Count: 3428 
• Modelled Residue Count: 381 
• Deposited Residue Count: 402 
• 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
• Primary Citation of Related Structures:  
  4MDI, 4MDJ, 4MCZ, 4MD4, 4MD5, 4MCY, 4MD0


• 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	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 histocompatibility antigen, DRB1-4 beta chain	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
Citrullinated Vimentin	C	13	Homo sapiens	Mutation(s): 0  Gene Names: VIM
UniProt & NIH Common Fund Data Resources
Find proteins for P08670 (Homo sapiens) Explore P08670  Go to UniProtKB:  P08670
PHAROS:  P08670 GTEx:  ENSG00000026025

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth B]	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: 2.41 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
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary