4OZI

S2 protein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.243 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.214 (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 1.7 of the entry. See complete history


Literature

T-cell receptor recognition of HLA-DQ2-gliadin complexes associated with celiac disease.

Petersen, J.Montserrat, V.Mujico, J.R.Loh, K.L.Beringer, D.X.van Lummel, M.Thompson, A.Mearin, M.L.Schweizer, J.Kooy-Winkelaar, Y.van Bergen, J.Drijfhout, J.W.Kan, W.T.La Gruta, N.L.Anderson, R.P.Reid, H.H.Koning, F.Rossjohn, J.

(2014) Nat Struct Mol Biol 21: 480-488

  • DOI: https://doi.org/10.1038/nsmb.2817
  • Primary Citation of Related Structures:  
    4OZF, 4OZG, 4OZH, 4OZI

  • PubMed Abstract: 

    Celiac disease is a T cell-mediated disease induced by dietary gluten, a component of which is gliadin. 95% of individuals with celiac disease carry the HLA (human leukocyte antigen)-DQ2 locus. Here we determined the T-cell receptor (TCR) usage and fine specificity of patient-derived T-cell clones specific for two epitopes from wheat gliadin, DQ2.5-glia-α1a and DQ2.5-glia-α2. We determined the ternary structures of four distinct biased TCRs specific for those epitopes. All three TCRs specific for DQ2.5-glia-α2 docked centrally above HLA-DQ2, which together with mutagenesis and affinity measurements provided a basis for the biased TCR usage. A non-germline encoded arginine residue within the CDR3β loop acted as the lynchpin within this common docking footprint. Although the TCRs specific for DQ2.5-glia-α1a and DQ2.5-glia-α2 docked similarly, their interactions with the respective gliadin determinants differed markedly, thereby providing a basis for epitope specificity.


  • Organizational Affiliation

    1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia. [2].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chain
A, C
191Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens)
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Go to UniProtKB:  P01909
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 chain
B, D
213Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
UniProt
Find proteins for Q5Y7D3 (Homo sapiens)
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UniProt GroupQ5Y7D3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor, s2, alpha chain
E, G
207Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q2YD82 (Homo sapiens)
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UniProt GroupQ2YD82
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor, s2, beta chain
F, H
244Homo 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
deamidated Gliadin-alpha1 peptide
I, J
13Triticum aestivumMutation(s): 0 
UniProt
Find proteins for P04722 (Triticum aestivum)
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UniProt GroupP04722
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.243 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 233.027α = 90
b = 142.239β = 109.79
c = 101.09γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

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: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-28
    Changes: Data collection
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2015-02-04
    Changes: Derived calculations
  • Version 1.4: 2015-04-22
    Changes: Database references
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.6: 2023-12-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.7: 2024-11-06
    Changes: Structure summary