5WKH

D30 TCR in complex with HLA-A*11:01-GTS3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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
  • Structures With Same Primary Citation

  • 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-chai ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-11 alpha chain
A, F
274Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, G
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GTS3 peptide
C, H
10Dengue virus 3Mutation(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 Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000))
Go to UniProtKB:  Q6YMS4
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
D30 TCR beta chain
E, J
244Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain
D, I
198Homo sapiensMutation(s): 1 
Gene Names: TRAV30
Find proteins for K7N5N2 (Homo sapiens)
Go to UniProtKB:  K7N5N2
Find proteins for A0A087WSZ9 (Homo sapiens)
Go to UniProtKB:  A0A087WSZ9
NIH Common Fund Data Resources
PHAROS  A0A087WSZ9
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.389α = 90
b = 170.536β = 113.89
c = 85.692γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata processing

Structure Validation

View Full Validation Report



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