4OZF

JR5.1 protein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

T-cell receptor recognition of HLA-DQ2-gliadin complexes associated with celiac disease.

Petersen, J.Montserrat, V.Mujico, J.R.Loh, K.L.Beringer, D.X.van Lummel, M.Thompson, A.Mearin, M.L.Schweizer, J.Kooy-Winkelaar, Y.van Bergen, J.Drijfhout, J.W.Kan, W.T.La Gruta, N.L.Anderson, R.P.Reid, H.H.Koning, F.Rossjohn, J.

(2014) Nat.Struct.Mol.Biol. 21: 480-488

  • DOI: 10.1038/nsmb.2817
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Celiac disease is a T cell-mediated disease induced by dietary gluten, a component of which is gliadin. 95% of individuals with celiac disease carry the HLA (human leukocyte antigen)-DQ2 locus. Here we determined the T-cell receptor (TCR) usage and f ...

    Celiac disease is a T cell-mediated disease induced by dietary gluten, a component of which is gliadin. 95% of individuals with celiac disease carry the HLA (human leukocyte antigen)-DQ2 locus. Here we determined the T-cell receptor (TCR) usage and fine specificity of patient-derived T-cell clones specific for two epitopes from wheat gliadin, DQ2.5-glia-α1a and DQ2.5-glia-α2. We determined the ternary structures of four distinct biased TCRs specific for those epitopes. All three TCRs specific for DQ2.5-glia-α2 docked centrally above HLA-DQ2, which together with mutagenesis and affinity measurements provided a basis for the biased TCR usage. A non-germline encoded arginine residue within the CDR3β loop acted as the lynchpin within this common docking footprint. Although the TCRs specific for DQ2.5-glia-α1a and DQ2.5-glia-α2 docked similarly, their interactions with the respective gliadin determinants differed markedly, thereby providing a basis for epitope specificity.


    Organizational Affiliation

    1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia. [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DQ alpha 1 chain
A
191Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
Find proteins for P01909 (Homo sapiens)
Go to Gene View: HLA-DQA1
Go to UniProtKB:  P01909
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DQ beta 1 chain
B
213Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
Find proteins for Q5Y7D3 (Homo sapiens)
Go to Gene View: HLA-DQB1
Go to UniProtKB:  Q5Y7D3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR, JR5.1 ALPHA CHAIN
G
202Homo sapiensMutation(s): 0 
Gene Names: TRA@
Find proteins for Q2YD82 (Homo sapiens)
Go to UniProtKB:  Q2YD82
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR, JR5.1 BETA CHAIN
H
244Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
deamidated Gliadin-alpha2 peptide
J
13Triticum aestivumMutation(s): 0 
Find proteins for P04722 (Triticum aestivum)
Go to UniProtKB:  P04722
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
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: 2.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.930α = 90.00
b = 84.840β = 92.99
c = 109.680γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-28
    Type: Data collection
  • Version 1.2: 2014-12-24
    Type: Database references
  • Version 1.3: 2015-02-04
    Type: Derived calculations
  • Version 1.4: 2015-04-22
    Type: Database references