5KSB

T15-DQ8.5-glia-gamma1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Diverse T Cell Receptor Gene Usage in HLA-DQ8-Associated Celiac Disease Converges into a Consensus Binding Solution.

Petersen, J.Kooy-Winkelaar, Y.Loh, K.L.Tran, M.van Bergen, J.Koning, F.Rossjohn, J.Reid, H.H.

(2016) Structure 24: 1643-1657

  • DOI: 10.1016/j.str.2016.07.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In HLA-DQ8-associated celiac disease, TRAV26-2+-TRBV9+ and TRAV8-3+-TRBV6+ T cells recognize the immunodominant DQ8-glia-α1 epitope, whereupon a non-germline-encoded arginine residue played a key role in binding HLA-DQ8-glia-α1. Whether distinct T ce ...

    In HLA-DQ8-associated celiac disease, TRAV26-2+-TRBV9+ and TRAV8-3+-TRBV6+ T cells recognize the immunodominant DQ8-glia-α1 epitope, whereupon a non-germline-encoded arginine residue played a key role in binding HLA-DQ8-glia-α1. Whether distinct T cell receptor (TCR) recognition modes exist for gliadin epitopes remains unclear. TCR repertoire analysis revealed populations of HLA-DQ8-glia-α1 and HLA-DQ8.5-glia-γ1 restricted TRAV20+-TRBV9+ T cells that did not possess a non-germline-encoded arginine residue. The crystal structures of a TRAV20+-TRBV9+ TCR-HLA-DQ8-glia-α1 complex and two TRAV20+-TRBV9+ TCR-HLA-DQ8.5-glia-γ1 complexes were determined. This revealed that the differential specificity toward DQ8-glia-α1 and DQ8.5-glia-γ1 was governed by CDR3β-loop-mediated interactions. Surprisingly, a germline-encoded arginine residue within the CDR1α loop of the TRAV20+ TCR substituted for the role of the non-germline-encoded arginine in the TRAV26-2+-TRBV9+ and TRAV8-3+-TRBV6+ TCRs. Thus, in celiac disease, the responding TCR repertoire is driven by a common mechanism that selects for structural elements within the TCR that have convergent binding solutions in HLA-DQ8-gliadin recognition.


    Organizational Affiliation

    Infection and Immunity Program, The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia.




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
225Homo sapiensTriticum aestivum
This entity is chimeric
Mutation(s): 0 
Gene Names: HLA-DQB1,
Find proteins for A0A0U5Q247 (Homo sapiens)
Go to Gene View: HLA-DQB1
Go to UniProtKB:  A0A0U5Q247
Find proteins for P08079 (Triticum aestivum)
Go to UniProtKB:  P08079
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T15 TCR alpha TRAV20*02
E, G
206Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA), TRAV20
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Find proteins for A0A0B4J274 (Homo sapiens)
Go to UniProtKB:  A0A0B4J274
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T15 TCR beta TRBV9*01
F, H
243Homo sapiensMutation(s): 0 
Gene Names: TRBV9 (TCRBV1S1A1N1), TRBC2 (TCRBC2)
Find proteins for A0A580 (Homo sapiens)
Go to UniProtKB:  A0A580
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DQ8.5-glia-gamma1 peptide
I, J
11Triticum aestivumMutation(s): 0 
Find proteins for P08079 (Triticum aestivum)
Go to UniProtKB:  P08079
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 115.890α = 90.00
b = 125.050β = 90.00
c = 165.630γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references