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 <sup>+ </sup>-TRBV9 <sup>+ </sup> and TRAV8-3 <sup>+ </sup>-TRBV6 <sup>+ </sup> T cells recognize the immunodominant DQ8-glia-α1 epitope, whereupon a non-germline-encoded arginine residue played a key ro ...

    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

    Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands. Electronic address: f.koning@lumc.nl.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.,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.,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; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK. Electronic address: jamie.rossjohn@monash.edu.,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. Electronic address: hugh.reid@monash.edu.




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