5KS9

Bel502-DQ8-glia-alpha1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  5KSA, 5KSB

  • 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
192Homo sapiensGene Names: HLA-DQA1
Find proteins for L8E864 (Homo sapiens)
Go to Gene View: HLA-DQA1
Go to UniProtKB:  L8E864
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DQ beta 1 chain
B, D
230Homo sapiensTriticum aestivum
This entity is chimeric
Gene Names: HLA-DQB1, gli-2
Find proteins for A0A0U5Q247 (Homo sapiens)
Go to Gene View: HLA-DQB1
Go to UniProtKB:  A0A0U5Q247
Find proteins for R9XSW3 (Triticum aestivum)
Go to UniProtKB:  R9XSW3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Bel502 TCR alpha TRAV20*01
E, G
207Homo sapiensGene 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
Bel502 TCR beta TRBV9*01
F, H
242Homo sapiensGene Names: TCRBV1S1A1N1 (TRBV9), 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-glia-alpha1 peptide
I, J
16Triticum aestivumN/A
Find proteins for P18573 (Triticum aestivum)
Go to UniProtKB:  P18573
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, E, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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: 2.55 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.560α = 90.00
b = 56.870β = 92.77
c = 232.050γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
BUSTERrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Health and Medical Research Council (Australia)AustraliaAPP1085875

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Data collection, Database references, Derived calculations