5WKF

D30 TCR in complex with HLA-A*11:01-GTS1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Germline bias dictates cross-serotype reactivity in a common dengue-virus-specific CD8(+) T cell response.

Culshaw, A.Ladell, K.Gras, S.McLaren, J.E.Miners, K.L.Farenc, C.van den Heuvel, H.Gostick, E.Dejnirattisai, W.Wangteeraprasert, A.Duangchinda, T.Chotiyarnwong, P.Limpitikul, W.Vasanawathana, S.Malasit, P.Dong, T.Rossjohn, J.Mongkolsapaya, J.Price, D.A.Screaton, G.R.

(2017) Nat Immunol 18: 1228-1237

  • DOI: https://doi.org/10.1038/ni.3850
  • Primary Citation of Related Structures:  
    5WJL, 5WJN, 5WKF, 5WKH

  • PubMed Abstract: 

    Adaptive immune responses protect against infection with dengue virus (DENV), yet cross-reactivity with distinct serotypes can precipitate life-threatening clinical disease. We found that clonotypes expressing the T cell antigen receptor (TCR) β-chain variable region 11 (TRBV11-2) were 'preferentially' activated and mobilized within immunodominant human-leukocyte-antigen-(HLA)-A*11:01-restricted CD8 + T cell populations specific for variants of the nonstructural protein epitope NS3 133 that characterize the serotypes DENV1, DENV3 and DENV4. In contrast, the NS3 133 -DENV2-specific repertoire was largely devoid of such TCRs. Structural analysis of a representative TRBV11-2 + TCR demonstrated that cross-serotype reactivity was governed by unique interplay between the variable antigenic determinant and germline-encoded residues in the second β-chain complementarity-determining region (CDR2β). Extensive mutagenesis studies of three distinct TRBV11-2 + TCRs further confirmed that antigen recognition was dependent on key contacts between the serotype-defined peptide and discrete residues in the CDR2β loop. Collectively, these data reveal an innate-like mode of epitope recognition with potential implications for the outcome of sequential exposure to heterologous DENVs.


  • Organizational Affiliation

    Department of Medicine, Imperial College London, London, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-11 alpha chain
A, F
274Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GTS1 peptide
C, H
10dengue virus type 1Mutation(s): 0 
UniProt
Find proteins for P17763 (Dengue virus type 1 (strain Nauru/West Pac/1974))
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UniProt GroupP17763
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain Chimera
D, I
198Homo sapiensMutation(s): 0 
Gene Names: TRAV30
UniProt & NIH Common Fund Data Resources
Find proteins for K7N5N2 (Homo sapiens)
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Find proteins for A0A087WSZ9 (Homo sapiens)
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PHAROS:  A0A087WSZ9
GTEx:  ENSG00000259092 
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UniProt GroupsK7N5N2A0A087WSZ9
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
D30 TCR beta chain
E, J
244Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.057α = 90
b = 146.376β = 90
c = 167.557γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata processing
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references
  • Version 1.2: 2017-10-25
    Changes: Database references