4OZG

D2 protein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report



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

  • 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 f ...

    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] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK. [3] Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia. [4] [5].



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chainAC191Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
Find proteins for P01909 (Homo sapiens)
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Go to UniProtKB:  P01909
NIH Common Fund Data Resources
PHAROS  P01909
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ beta 1 chainBD213Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
Find proteins for Q5Y7D3 (Homo sapiens)
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Go to UniProtKB:  Q5Y7D3
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor, d2, alpha chainEG202Homo sapiensMutation(s): 0 
Gene Names: TRA@
Find proteins for Q2YD82 (Homo sapiens)
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Go to UniProtKB:  Q2YD82
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor, d2, beta chainFH242Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
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Go to UniProtKB:  P01850
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
deamidated Gliadin-alpha2 peptideIJ13Triticum aestivumMutation(s): 0 
Find proteins for P04722 (Triticum aestivum)
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Go to UniProtKB:  P04722
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, L
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 266.024α = 90
b = 60.266β = 114.04
c = 138.235γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary