5KSA

Bel602-DQ8.5-glia-gamma1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1016/j.str.2016.07.010
  • Primary Citation of Related Structures:  
    5KS9, 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chain191Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens)
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PHAROS:  P01909
GTEx:  ENSG00000196735 
Entity Groups  
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UniProt GroupP01909
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ beta 1 chain225Triticum aestivumHomo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for P08079 (Triticum aestivum)
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Find proteins for A0A0U5Q247 (Homo sapiens)
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UniProt GroupsP08079A0A0U5Q247
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Bel602 alpha TRAV20*01206Homo sapiensMutation(s): 0 
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PHAROS:  A0A0B4J274
GTEx:  ENSG00000211800 
Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupsP01848A0A0B4J274
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Bel602 beta TRBV9*01243Homo sapiensMutation(s): 0 
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Find proteins for A0A5B9 (Homo sapiens)
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PHAROS:  A0A5B9
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UniProt GroupsA0A580A0A5B9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DQ8.5-glia-gamma1 peptideE [auth J]11Triticum aestivumMutation(s): 0 
UniProt
Find proteins for P08079 (Triticum aestivum)
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UniProt GroupP08079
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.548α = 90
b = 98.831β = 95.69
c = 80.175γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary