5WJN | pdb_00005wjn

Crystal Structure of HLA-A*11:01-GTS3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.230 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.201 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5WJN

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: 133.86 kDa 
  • Atom Count: 9,779 
  • Modeled Residue Count: 1,152 
  • Deposited Residue Count: 1,152 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-11 alpha chain
A, D, G
274Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E, H
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
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UniProt GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
GTS3 peptide
C, F, I
10dengue virus type 3Mutation(s): 0 
UniProt
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000))
Explore Q6YMS4 
Go to UniProtKB:  Q6YMS4
Entity Groups
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UniProt GroupQ6YMS4
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K

Query on K



Download:Ideal Coordinates CCD File
J [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.230 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.201 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.325α = 90
b = 145.522β = 121.14
c = 106.303γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata processing

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: 2024-10-23
    Changes: Data collection, Database references, Structure summary