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

  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-11 alpha chainA, F274Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
GTEx  ENSG00000206503
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, G100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
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Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
GTEx  ENSG00000166710
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GTS1 peptideC, H10Dengue virus 1Mutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P17763 (Dengue virus type 1 (strain Nauru/West Pac/1974))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain ChimeraD, I198Homo sapiensMutation(s): 0 
Gene Names: TRAV30
Find proteins for K7N5N2 (Homo sapiens)
Explore K7N5N2 
Go to UniProtKB:  K7N5N2
Find proteins for A0A087WSZ9 (Homo sapiens)
Explore A0A087WSZ9 
Go to UniProtKB:  A0A087WSZ9
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PHAROS  A0A087WSZ9
GTEx  ENSG00000259092
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
D30 TCR beta chainE, J244Homo sapiensMutation(s): 0 
Protein Feature View
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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

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2017-07-25 
  • Released Date: 2017-09-20 
    • Deposition Author(s): Gras, S., Rossjohn, J.

Revision History 

  • 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