6KX9

Crystal structure of 8-mer peptide from avian influenza H5N1 virus in complex with BF2*1501


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the MHC-I molecule BF2*1501 disclose the preferred presentation of an H5N1 virus-derived epitope.

Li, X.Zhang, L.Liu, Y.Ma, L.Zhang, N.Xia, C.

(2020) J Biol Chem 295: 5292-5306

  • DOI: https://doi.org/10.1074/jbc.RA120.012713
  • Primary Citation of Related Structures:  
    6IRL, 6KX9

  • PubMed Abstract: 

    Lethal infections by strains of the highly-pathogenic avian influenza virus (HPAIV) H5N1 pose serious threats to both the poultry industry and public health worldwide. A lack of confirmed HPAIV epitopes recognized by cytotoxic T lymphocytes (CTLs) has hindered the utilization of CD8 + T-cell-mediated immunity and has precluded the development of effectively diversified epitope-based vaccination approaches. In particular, an HPAIV H5N1 CTL-recognized epitope based on the peptide MHC-I-β2m (pMHC-I) complex has not yet been designed. Here, screening a collection of selected peptides of several HPAIV strains against a specific pathogen-free pMHC-I (pBF2*1501), we identified a highly-conserved HPAIV H5N1 CTL epitope, named HPAIV-PA 123-130 We determined the structure of the BF2*1501-PA 123-130 complex at 2.1 Å resolution to elucidate the molecular mechanisms of a preferential presentation of the highly-conserved PA 123-130 epitope in the chicken B15 lineage. Conformational characteristics of the PA 123-130 epitope with a protruding Tyr-7 residue indicated that this epitope has great potential to be recognized by specific TCRs. Moreover, significantly increased numbers of CD8 + T cells specific for the HPAIV-PA 123-130 epitope in peptide-immunized chickens indicated that a repertoire of CD8 + T cells can specifically respond to this epitope. We anticipate that the identification and structural characterization of the PA 123-130 epitope reported here could enable further studies of CTL immunity against HPAIV H5N1. Such studies may aid in the development of vaccine development strategies using well-conserved internal viral antigens in chickens.


  • Organizational Affiliation

    Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, People's Republic of China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I272Gallus gallusMutation(s): 0 
Gene Names: BF2
UniProt
Find proteins for Q9GIP6 (Gallus gallus)
Explore Q9GIP6 
Go to UniProtKB:  Q9GIP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GIP6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Gallus gallusMutation(s): 0 
Gene Names: B2M
UniProt
Find proteins for P21611 (Gallus gallus)
Explore P21611 
Go to UniProtKB:  P21611
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21611
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
8-pepide (ARG-ARG-ALA-LEU-ARG-GLU-GLY-TYR)8synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.195α = 90
b = 124.195β = 90
c = 80.57γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31572493

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description