5SWS

Crystal Structure of NP2-B17 TCR-H2Db-NP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reversed T Cell Receptor Docking on a Major Histocompatibility Class I Complex Limits Involvement in the Immune Response.

Gras, S.Chadderton, J.Del Campo, C.M.Farenc, C.Wiede, F.Josephs, T.M.Sng, X.Y.Mirams, M.Watson, K.A.Tiganis, T.Quinn, K.M.Rossjohn, J.La Gruta, N.L.

(2016) Immunity 45: 749-760

  • DOI: 10.1016/j.immuni.2016.09.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The anti-viral T cell response is drawn from the naive T cell repertoire. During influenza infection, the CD8 <sup>+ </sup> T cell response to an H-2D <sup>b </sup>-restricted nucleoprotein epitope (NP <sub>366 </sub>) is characterized by preferentia ...

    The anti-viral T cell response is drawn from the naive T cell repertoire. During influenza infection, the CD8 + T cell response to an H-2D b -restricted nucleoprotein epitope (NP 366 ) is characterized by preferential expansion of T cells bearing TRBV13 + T cell receptors (TCRs) and avoidance of TRBV17 + T cells, despite the latter dominating the naive precursor repertoire. We found two TRBV17 + TCRs that bound H-2D b -NP 366 with a 180° reversed polarity compared to the canonical TCR-pMHC-I docking. The TRBV17 β-chain dominated the interaction and, whereas the complementarity determining region-3 (CDR3) loops exclusively mediated contacts with the MHC-I, peptide specificity was attributable to germline-encoded recognition. Nevertheless, the TRBV17 + TCR exhibited moderate affinity toward H-2D b -NP 366 and was capable of signal transduction. Thus, the naive CD8 + T cell pool can comprise TCRs adopting reversed pMHC-I docking modes that limit their involvement in the immune response.


    Organizational Affiliation

    Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK. Electronic address: jamie.rossjohn@monash.edu.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: nicole.la.gruta@monash.edu.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3010, Australia.,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3010, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen, D-B alpha chain
A
280Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
Go to UniProtKB:  P01899
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
influenza NP366 epitope
C
9Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)Mutation(s): 0 
Gene Names: NP
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Go to UniProtKB:  Q9Q0U8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NP1-B17 TCR alpha chain
D
207N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NP1-B17 TCR beta chain
E
242N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.017α = 90.00
b = 126.942β = 105.66
c = 80.479γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Data collection, Database references, Derived calculations, Refinement description