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 5WWU | pdb_00005wwu

Crystal Structure of HLA-A*2402 in complex with 2009 pandemic influenza A(H1N1) virus and avian influenza A(H5N1) virus-derived peptide H1-25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 
    0.284 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5WWU

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

Literature

Heterosubtypic Protections against Human-Infecting Avian Influenza Viruses Correlate to Biased Cross-T-Cell Responses.

Zhao, M., Liu, K., Luo, J., Tan, S., Quan, C., Zhang, S., Chai, Y., Qi, J., Li, Y., Bi, Y., Xiao, H., Wong, G., Zhou, J., Jiang, T., Liu, W., Yu, H., Yan, J., Liu, Y., Shu, Y., Wu, G., Wu, A., Gao, G.F., Liu, W.J.

(2018) mBio 9

  • DOI: https://doi.org/10.1128/mBio.01408-18
  • Primary Citation Related Structures: 
    5WWU, 5WXC, 5WXD

  • PubMed Abstract: 

    Against a backdrop of seasonal influenza virus epidemics, emerging avian influenza viruses (AIVs) occasionally jump from birds to humans, posing a public health risk, especially with the recent sharp increase in H7N9 infections. Evaluations of cross-reactive T-cell immunity to seasonal influenza viruses and human-infecting AIVs have been reported previously. However, the roles of influenza A virus-derived epitopes in the cross-reactive T-cell responses and heterosubtypic protections are not well understood; understanding those roles is important for preventing and controlling new emerging AIVs. Here, among the members of a healthy population presumed to have previously been infected by pandemic H1N1 (pH1N1), we found that pH1N1-specific T cells showed cross- but biased reactivity to human-infecting AIVs, i.e., H5N1, H6N1, H7N9, and H9N2, which correlates with distinct protections. Through a T-cell epitope-based phylogenetic analysis, the cellular immunogenic clustering expanded the relevant conclusions to a broader range of virus strains. We defined the potential key conserved epitopes required for cross-protection and revealed the molecular basis for the immunogenic variations. Our study elucidated an overall profile of cross-reactivity to AIVs and provided useful recommendations for broad-spectrum vaccine development. IMPORTANCE We revealed preexisting but biased T-cell reactivity of pH1N1 influenza virus to human-infecting AIVs, which provided distinct protections. The cross-reactive T-cell recognition had a regular pattern that depended on the T-cell epitope matrix revealed via bioinformatics analysis. Our study elucidated an overall profile of cross-reactivity to AIVs and provided useful recommendations for broad-spectrum vaccine development.


  • Organizational Affiliation: 
    • CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 44.74 kDa 
  • Atom Count: 3,150 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 384 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-24 alpha chain274Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
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UniProt GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LEU-TYR-LYS-LYS-LEU-LYS-ARG-GLU-ILE-THR-PHEC [auth E]11Influenza A virus (A/chicken/China/028/2014(H7N9))Mutation(s): 0 
UniProt
Find proteins for A0A0X9JHC1 (Influenza A virus)
Explore A0A0X9JHC1 
Go to UniProtKB:  A0A0X9JHC1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X9JHC1
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free:  0.284 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.752α = 90
b = 79.099β = 90
c = 88.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSdata reduction
CNSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary