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 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.4 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

    Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands. Electronic address: f.koning@lumc.nl.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chain
A, C
192Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt
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UniProt GroupL8E864
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ beta 1 chain
B, D
230Triticum aestivumHomo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt
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UniProt GroupsA0A0U5Q247R9XSW3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Bel502 TCR alpha TRAV20*01
E, G
207Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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PHAROS:  A0A0B4J274
GTEx:  ENSG00000211800 
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PHAROS:  P01848
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UniProt GroupsP01848A0A0B4J274
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Bel502 TCR beta TRBV9*01
F, H
242Homo 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-glia-alpha1 peptide
I, J
16Triticum aestivumMutation(s): 0 
UniProt
Find proteins for P18573 (Triticum aestivum)
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UniProt GroupP18573
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.56α = 90
b = 56.87β = 92.77
c = 232.05γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1085875

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: 2017-09-06
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary