4OZG

D2 protein complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 

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, C
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, D
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, d2, alpha chain
E, 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, d2, beta chain
F, H
242Homo 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
I, J
13Triticum aestivumMutation(s): 0 
Find proteins for P04722 (Triticum aestivum)
Go to UniProtKB:  P04722
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 266.024α = 90.00
b = 60.266β = 114.04
c = 138.235γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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