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 5WKF | pdb_00005wkf

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 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5WKF

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 187.78 kDa 
  • Atom Count: 13,580 
  • Modeled Residue Count: 1,651 
  • Deposited Residue Count: 1,652 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-11 alpha chain
A, F
274Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
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UniProt GroupP04439
Sequence Annotations
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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: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  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))
Explore P17763 
Go to UniProtKB:  P17763
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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 A0A087WSZ9 (Homo sapiens)
Explore A0A087WSZ9 
Go to UniProtKB:  A0A087WSZ9
GTEx:  ENSG00000259092 
Find proteins for K7N5N2 (Homo sapiens)
Explore K7N5N2 
Go to UniProtKB:  K7N5N2
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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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.253 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
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
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Structure summary