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


Ligand Structure Quality Assessment 


This is version 2.1 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

    Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands.


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
GTEx:  ENSG00000196735 
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UniProt GroupP01909
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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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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor, d2, alpha chain
E, G
202Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q2YD82 (Homo sapiens)
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Go to UniProtKB:  Q2YD82
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UniProt GroupQ2YD82
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor, d2, beta chain
F, H
242Homo 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-alpha2 peptide
I, J
13Triticum aestivumMutation(s): 0 
UniProt
Find proteins for P04722 (Triticum aestivum)
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UniProt GroupP04722
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
N [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
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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Ligand Structure Quality Assessment 


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 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
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Structure summary