4L8D

Crystal structure of the H2Db in complex with the NP-N5D peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Acute emergence and reversion of influenza A virus quasispecies within CD8(+) T cell antigenic peptides.

Valkenburg, S.A., Quinones-Parra, S., Gras, S., Komadina, N., McVernon, J., Wang, Z., Halim, H., Iannello, P., Cole, C., Laurie, K., Kelso, A., Rossjohn, J., Doherty, P.C., Turner, S.J., Kedzierska, K.

(2013) Nat Commun 4: 2663-2663

  • DOI: 10.1038/ncomms3663
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Influenza A virus-specific CD8(+) cytotoxic T lymphocytes (CTLs) provide a degree of cross-strain protection that is potentially subverted by mutation. Here we describe the sequential emergence of such variants within CTL epitopes for a persistently ...

    Influenza A virus-specific CD8(+) cytotoxic T lymphocytes (CTLs) provide a degree of cross-strain protection that is potentially subverted by mutation. Here we describe the sequential emergence of such variants within CTL epitopes for a persistently infected, immunocompromised infant. Further analysis in immunodeficient and wild-type mice supports the view that CTL escape variants arise frequently in influenza, accumulate with time and revert in the absence of immune pressure under MHCI-mismatched conditions. Viral fitness, the abundance of endogenous CD8(+) T cell responses and T cell receptor repertoire diversity influence the nature of these de novo mutants. Structural characterization of dominant escape variants shows how the peptide-MHCI interaction is modified to affect variant-MHCI stability. The mechanism of influenza virus escape thus looks comparable to that recognized for chronic RNA viruses like HIV and HCV, suggesting that immunocompromised patients with prolonged viral infection could have an important part in the emergence of influenza quasispecies.

    Organizational Affiliation: 

    Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 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, C
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, D
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NP-N5D peptide
E, F
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.343α = 90.00
b = 136.132β = 90.00
c = 80.874γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling
BUSTER-TNTrefinement
PHASERphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2013-06-16 
  • Released Date: 2013-10-16 
  • Deposition Author(s): Rossjohn, J., Gras, S.

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-12-04
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description