5KSA

Bel602-DQ8.5-glia-gamma1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.3 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
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PHAROS:  P01909
GTEx:  ENSG00000196735 
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UniProt GroupP01909
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01909-1
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
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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 
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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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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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Go to UniProtKB:  P08079
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UniProt GroupP08079
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

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
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary