7MLE | pdb_00007mle

Crystal Structure of HLA-A*03:01 in complex with VVRPSVASK, an 9-mer epitope from Influenza B virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.264 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Homologous peptides derived from influenza A, B and C viruses induce variable CD8 + T cell responses with cross-reactive potential.

Nguyen, A.T.Lau, H.M.P.Sloane, H.Jayasinghe, D.Mifsud, N.A.Chatzileontiadou, D.S.Grant, E.J.Szeto, C.Gras, S.

(2022) Clin Transl Immunology 11: e1422-e1422

  • DOI: https://doi.org/10.1002/cti2.1422
  • Primary Citation Related Structures: 
    7MLE

  • PubMed Abstract: 

    Influenza A, B and C viruses (IAV, IBV and ICV, respectively) circulate globally, infecting humans and causing widespread morbidity and mortality. Here, we investigate the T cell response towards an immunodominant IAV epitope, NP 265-273, and its IBV and ICV homologues, presented by HLA-A*03:01 molecule expressed in ~ 4% of the global population (~ 300 million people). We assessed the magnitude (tetramer staining) and quality of the CD8 + T cell response (intracellular cytokine staining) towards NP 265-IAV and described the T cell receptor (TCR) repertoire used to recognise this immunodominant epitope. We next assessed the immunogenicity of NP 265-IAV homologue peptides from IBV and ICV and the ability of CD8 + T cells to cross-react towards these homologous peptides. Furthermore, we determined the structures of NP 265-IAV and NP 323-IBV peptides in complex with HLA-A*03:01 by X-ray crystallography. Our study provides a detailed characterisation of the CD8 + T cell response towards NP 265-IAV and its IBV and ICV homologues. The data revealed a diverse repertoire for NP 265-IAV that is associated with superior anti-viral protection. Evidence of cross-reactivity between the three different influenza virus strain-derived epitopes was observed, indicating the discovery of a potential vaccination target that is broad enough to cover all three influenza strains. We show that while there is a potential to cross-protect against distinct influenza virus lineages, the T cell response was stronger against the IAV peptide than IBV or ICV, which is an important consideration when choosing targets for future vaccine design.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University Clayton VIC Australia.

Macromolecule Content 

  • Total Structure Weight: 45.07 kDa 
  • Atom Count: 3,508 
  • Modeled Residue Count: 386 
  • Deposited Residue Count: 386 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A alpha chain277Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
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-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein peptide9Influenza B virusMutation(s): 0 
UniProt
Find proteins for P13884 (Influenza B virus (strain B/Ann Arbor/1/1966 [cold-adapted]))
Explore P13884 
Go to UniProtKB:  P13884
Entity Groups
UniProt GroupP13884
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.264 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.265α = 90
b = 155.265β = 90
c = 85.331γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1159272

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary