4NQX

Crystal Structure of HLA A*0101 in complex with NP44-S7N, an 9-mer influenza epitope


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Preexisting CD8+ T-cell immunity to the H7N9 influenza A virus varies across ethnicities.

Quinones-Parra, S.Grant, E.Loh, L.Nguyen, T.H.Campbell, K.A.Tong, S.Y.Miller, A.Doherty, P.C.Vijaykrishna, D.Rossjohn, J.Gras, S.Kedzierska, K.

(2014) Proc Natl Acad Sci U S A 111: 1049-1054

  • DOI: 10.1073/pnas.1322229111
  • Primary Citation of Related Structures:  
    4NQV, 4NQX

  • PubMed Abstract: 
  • The absence of preexisting neutralizing antibodies specific for the novel A (H7N9) influenza virus indicates a lack of prior human exposure. As influenza A virus-specific CD8(+) T lymphocytes (CTLs) can be broadly cross-reactive, we tested whether im ...

    The absence of preexisting neutralizing antibodies specific for the novel A (H7N9) influenza virus indicates a lack of prior human exposure. As influenza A virus-specific CD8(+) T lymphocytes (CTLs) can be broadly cross-reactive, we tested whether immunogenic peptides derived from H7N9 might be recognized by memory CTLs established following infection with other influenza strains. Probing across multiple ethnicities, we identified 32 conserved epitopes derived from the nucleoprotein (NP) and matrix-1 (M1) proteins. These NP and M1 peptides are presented by HLAs prevalent in 16-57% of individuals. Remarkably, some HLA alleles (A*0201, A*0301, B*5701, B*1801, and B*0801) elicit robust CTL responses against any human influenza A virus, including H7N9, whereas ethnicities where HLA-A*0101, A*6801, B*1501, and A*2402 are prominent, show limited CTL response profiles. By this criterion, some groups, especially the Alaskan and Australian Indigenous peoples, would be particularly vulnerable to H7N9 infection. This dissection of CTL-mediated immunity to H7N9 thus suggests strategies for both vaccine delivery and development.


    Organizational Affiliation

    Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, 3010, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-1 alpha chainACEGIK284Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBDFHJL100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NP44-S7N mutant peptide, CTELKLNDYMNOPQR9H7N9 subtypeMutation(s): 0 
Find proteins for Q07FI1 (Influenza A virus (strain A/China:Nanchang/11/1996 H1N1))
Explore Q07FI1 
Go to UniProtKB:  Q07FI1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.61α = 90
b = 81.411β = 121.82
c = 140.29γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-11-26 
  • Released Date: 2013-12-25 
  • Deposition Author(s): Rossjohn, J., Gras, S.

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references