4Z7U

S13 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Determinants of Gliadin-Specific T Cell Selection in Celiac Disease.

Petersen, J.van Bergen, J.Loh, K.L.Kooy-Winkelaar, Y.Beringer, D.X.Thompson, A.Bakker, S.F.Mulder, C.J.Ladell, K.McLaren, J.E.Price, D.A.Rossjohn, J.Reid, H.H.Koning, F.

(2015) J Immunol 194: 6112-6122

  • DOI: 10.4049/jimmunol.1500161
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In HLA-DQ8-associated celiac disease (CD), the pathogenic T cell response is directed toward an immunodominant α-gliadin-derived peptide (DQ8-glia-α1). However, our knowledge of TCR gene usage within the primary intestinal tissue of HLA-DQ8 (+) CD pa ...

    In HLA-DQ8-associated celiac disease (CD), the pathogenic T cell response is directed toward an immunodominant α-gliadin-derived peptide (DQ8-glia-α1). However, our knowledge of TCR gene usage within the primary intestinal tissue of HLA-DQ8 (+) CD patients is limited. We identified two populations of HLA-DQ8-glia-α1 tetramer(+) CD4(+) T cells that were essentially undetectable in biopsy samples from patients on a gluten-free diet but expanded rapidly and specifically after antigenic stimulation. Distinguished by expression of TRBV9, both T cell populations displayed biased clonotypic repertoires and reacted similarly against HLA-DQ8-glia-α1. In particular, TRBV9 paired most often with TRAV26-2, whereas the majority of TRBV9(-) TCRs used TRBV6-1 with no clear TRAV gene preference. Strikingly, both tetramer(+)/TRBV9(+) and tetramer(+)/TRBV9(-) T cells possessed a non-germline-encoded arginine residue in their CDR3α and CDR3β loops, respectively. Comparison of the crystal structures of three TRBV9(+) TCRs and a TRBV9(-) TCR revealed that, as a result of distinct TCR docking modes, the HLA-DQ8-glia-α1 contacts mediated by the CDR3-encoded arginine were almost identical between TRBV9(+) and TRBV9(-) TCRs. In all cases, this interaction centered on two hydrogen bonds with a specific serine residue in the bound peptide. Replacement of serine with alanine at this position abrogated TRBV9(+) and TRBV9(-) clonal T cell proliferation in response to HLA-DQ8-glia-α1. Gluten-specific memory CD4(+) T cells with structurally and functionally conserved TCRs therefore predominate in the disease-affected tissue of patients with HLA-DQ8-mediated CD.


    Organizational Affiliation

    Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands; jamie.rossjohn@monash.edu hugh.reid@monash.edu F.Koning@lumc.nl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class II HLA-DQ-alpha chain
A, C
192Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
Find proteins for Q30069 (Homo sapiens)
Go to UniProtKB:  Q30069
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR, S13 ALPHA CHAIN
E, G
203Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR, S13 BETA CHAIN
F, H
245Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
deamidated DQ8-glia-alpha1 peptide
I, J
18Triticum aestivumMutation(s): 0 
Find proteins for P18573 (Triticum aestivum)
Go to UniProtKB:  P18573
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II HLA-DQ-beta-1
B, D
213Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
Find proteins for O19707 (Homo sapiens)
Go to UniProtKB:  O19707
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
B, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.454α = 90
b = 123.813β = 90
c = 223.086γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references