4GG6

Protein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.285 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Models: experimental
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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 1.4 of the entry. See complete history


Literature

Biased T cell receptor usage directed against human leukocyte antigen DQ8-restricted gliadin peptides is associated with celiac disease.

Broughton, S.E.Petersen, J.Theodossis, A.Scally, S.W.Loh, K.L.Thompson, A.van Bergen, J.Kooy-Winkelaar, Y.Henderson, K.N.Beddoe, T.Tye-Din, J.A.Mannering, S.I.Purcell, A.W.McCluskey, J.Anderson, R.P.Koning, F.Reid, H.H.Rossjohn, J.

(2012) Immunity 37: 611-621

  • DOI: https://doi.org/10.1016/j.immuni.2012.07.013
  • Primary Citation of Related Structures:  
    4GG6, 4GG8

  • PubMed Abstract: 

    Celiac disease is a human leukocyte antigen (HLA)-DQ2- and/or DQ8-associated T cell-mediated disorder that is induced by dietary gluten. Although it is established how gluten peptides bind HLA-DQ8 and HLA-DQ2, it is unclear how such peptide-HLA complexes are engaged by the T cell receptor (TCR), a recognition event that triggers disease pathology. We show that biased TCR usage (TRBV9(∗)01) underpins the recognition of HLA-DQ8-α-I-gliadin. The structure of a prototypical TRBV9(∗)01-TCR-HLA-DQ8-α-I-gliadin complex shows that the TCR docks centrally above HLA-DQ8-α-I-gliadin, in which all complementarity-determining region-β (CDRβ) loops interact with the gliadin peptide. Mutagenesis at the TRBV9(∗)01-TCR-HLA-DQ8-α-I-gliadin interface provides an energetic basis for the Vβ bias. Moreover, CDR3 diversity accounts for TRBV9(∗)01(+) TCRs exhibiting differing reactivities toward the gliadin epitopes at various deamidation states. Accordingly, biased TCR usage is an important factor in the pathogenesis of DQ8-mediated celiac disease.


  • Organizational Affiliation

    The Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia.


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 & 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
Glycosylation
Glycosylation Sites: 2Go 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 chain
B, D
215Homo sapiensMutation(s): 0 
Gene Names: HLA-DQBHLA-DQB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01920 (Homo sapiens)
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PHAROS:  P01920
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UniProt GroupP01920
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
E, G
207Homo sapiensMutation(s): 0 
UniProt
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UniProt GroupK7N5N2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR, SP3.4 BETA CHAIN
F, H
245Homo sapiensMutation(s): 0 
UniProt
Find proteins for P01850 (Homo sapiens)
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UniProt GroupP01850
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Alpha/beta-gliadin MM1
I, J
18Triticum aestivumMutation(s): 2 
UniProt
Find proteins for P18573 (Triticum aestivum)
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UniProt GroupP18573
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.285 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.708α = 90
b = 134.325β = 90
c = 140.304γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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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: 2012-10-24
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2022-08-24
    Changes: Database references, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary