7SG1 | pdb_00007sg1

XPA5 TCR in complex with HLA-DQ2-alpha1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis of T cell receptor specificity and cross-reactivity of two HLA-DQ2.5-restricted gluten epitopes in celiac disease.

Ciacchi, L.Farenc, C.Dahal-Koirala, S.Petersen, J.Sollid, L.M.Reid, H.H.Rossjohn, J.

(2022) J Biological Chem 298: 101619-101619

  • DOI: https://doi.org/10.1016/j.jbc.2022.101619
  • Primary Citation of Related Structures:  
    7SG0, 7SG1, 7SG2

  • PubMed Abstract: 

    Celiac disease is a T cell-mediated chronic inflammatory condition often characterized by human leukocyte antigen (HLA)-DQ2.5 molecules presenting gluten epitopes derived from wheat, barley, and rye. Although some T cells exhibit cross-reactivity toward distinct gluten epitopes, the structural basis underpinning such cross-reactivity is unclear. Here, we investigated the T-cell receptor specificity and cross-reactivity of two immunodominant wheat gluten epitopes, DQ2.5-glia-α1a (PFPQPELPY) and DQ2.5-glia-ω1 (PFPQPEQPF). We show by surface plasmon resonance that a T-cell receptor alpha variable (TRAV) 4 + -T-cell receptor beta variable (TRBV) 29-1 + TCR bound to HLA-DQ2.5-glia-α1a and HLA-DQ2.5-glia-ω1 with similar affinity, whereas a TRAV4 - (TRAV9-2 + ) TCR recognized HLA-DQ2.5-glia-ω1 only. We further determined the crystal structures of the TRAV4 + -TRBV29-1 + TCR bound to HLA-DQ2.5-glia-α1a and HLA-DQ2.5-glia-ω1, as well as the structure of an epitope-specific TRAV9-2 + -TRBV7-3 + TCR-HLA-DQ2.5-glia-ω1 complex. We found that position 7 (p7) of the DQ2.5-glia-α1a and DQ2.5-glia-ω1 epitopes made very limited contacts with the TRAV4 + TCR, thereby explaining the TCR cross-reactivity across these two epitopes. In contrast, within the TRAV9-2 + TCR-HLA-DQ2.5-glia-ω1 ternary complex, the p7-Gln was situated in an electrostatic pocket formed by the hypervariable CDR3β loop of the TCR and Arg70β from HLA-DQ2.5, a polar network which would not be supported by the p7-Leu residue of DQ2.5-glia-α1a. In conclusion, we provide additional insights into the molecular determinants of TCR specificity and cross-reactivity to two closely-related epitopes in celiac disease.


  • Organizational Affiliation

    Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chainA,
C [auth F]
183Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens)
Explore P01909 
Go to UniProtKB:  P01909
PHAROS:  P01909
GTEx:  ENSG00000196735 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
MHC class II HLA-DQ-beta-1B,
D [auth G]
202Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
UniProt
Find proteins for Q5Y7D3 (Homo sapiens)
Explore Q5Y7D3 
Go to UniProtKB:  Q5Y7D3
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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, xpa5, alpha chainE [auth D],
I
203Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor, xpa5, beta chainF [auth E],
J
259Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DQ2-glia-alpha1a peptideG [auth C],
H
16Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth A],
N [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
L [auth A],
O [auth F],
P [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.602α = 90
b = 75.558β = 103.76
c = 216.804γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

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 & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-10-18
    Changes: Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary