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 
  • R-Value Observed: 0.233 

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:  
    5SWS, 5SWZ

  • PubMed Abstract: 
  • 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 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; 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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chainA280Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
influenza NP366 epitopeC9unidentified influenza virusMutation(s): 0 
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Explore Q9Q0U8 
Go to UniProtKB:  Q9Q0U8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NP1-B17 TCR alpha chainD207Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NP1-B17 TCR beta chainE242Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.017α = 90
b = 126.942β = 105.66
c = 80.479γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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