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 5SWS | pdb_00005sws

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 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5SWS

This is version 1.4 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: https://doi.org/10.1016/j.immuni.2016.09.007
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 95.95 kDa 
  • Atom Count: 6,758 
  • Modeled Residue Count: 816 
  • Deposited Residue Count: 837 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chain280Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Entity Groups
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UniProt GroupP01899
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
influenza NP366 epitope9unidentified influenza virusMutation(s): 0 
UniProt
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Explore Q9Q0U8 
Go to UniProtKB:  Q9Q0U8
Entity Groups
UniProt GroupQ9Q0U8
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NP1-B17 TCR alpha chain207Mus musculusMutation(s): 0 
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Sequence Annotations
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NP1-B17 TCR beta chain242Mus musculusMutation(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: 2.86 Å
  • R-Value Free:  0.274 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary