5SWZ

Crystal Structure of NP1-B17 TCR-H2Db-NP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

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: https://doi.org/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 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chain
A, F, K, P
280Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
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UniProt GroupP01899
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G, L, Q
99Mus 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 epitope
C, H, M, R
9unidentified 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 chain
D, I, N, S
207Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NP1-B17 TCR beta chain
E, J, O, T
243Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth O],
CA [auth T],
U [auth D],
V [auth E],
Z [auth K]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth K]
DA [auth T]
EA [auth T]
W [auth E]
X [auth I]
AA [auth K],
DA [auth T],
EA [auth T],
W [auth E],
X [auth I],
Y [auth J]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.231α = 90
b = 100.185β = 90
c = 469.456γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
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: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description