7JYW

Crystal Structure of HLA A*2402 in complex with TYQWIIRNW, an 9-mer influenza epitope


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

CD8 + T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph.

Hensen, L.Illing, P.T.Bridie Clemens, E.Nguyen, T.H.O.Koutsakos, M.van de Sandt, C.E.Mifsud, N.A.Nguyen, A.T.Szeto, C.Chua, B.Y.Halim, H.Rizzetto, S.Luciani, F.Loh, L.Grant, E.J.Saunders, P.M.Brooks, A.G.Rockman, S.Kotsimbos, T.C.Cheng, A.C.Richards, M.Westall, G.P.Wakim, L.M.Loudovaris, T.Mannering, S.I.Elliott, M.Tangye, S.G.Jackson, D.C.Flanagan, K.L.Rossjohn, J.Gras, S.Davies, J.Miller, A.Tong, S.Y.C.Purcell, A.W.Kedzierska, K.

(2021) Nat Commun 12: 2931-2931

  • DOI: https://doi.org/10.1038/s41467-021-23212-x
  • Primary Citation of Related Structures:  
    6XQA, 7JYU, 7JYV, 7JYW, 7JYX

  • PubMed Abstract: 

    Indigenous people worldwide are at high risk of developing severe influenza disease. HLA-A*24:02 allele, highly prevalent in Indigenous populations, is associated with influenza-induced mortality, although the basis for this association is unclear. Here, we define CD8 + T-cell immune landscapes against influenza A (IAV) and B (IBV) viruses in HLA-A*24:02-expressing Indigenous and non-Indigenous individuals, human tissues, influenza-infected patients and HLA-A*24:02-transgenic mice. We identify immunodominant protective CD8 + T-cell epitopes, one towards IAV and six towards IBV, with A24/PB2 550-558 -specific CD8 + T cells being cross-reactive between IAV and IBV. Memory CD8 + T cells towards these specificities are present in blood (CD27 + CD45RA - phenotype) and tissues (CD103 + CD69 + phenotype) of healthy individuals, and effector CD27 - CD45RA - PD-1 + CD38 + CD8 + T cells in IAV/IBV patients. Our data show influenza-specific CD8 + T-cell responses in Indigenous Australians, and advocate for T-cell-mediated vaccines that target and boost the breadth of IAV/IBV-specific CD8 + T cells to protect high-risk HLA-A*24:02-expressing Indigenous and non-Indigenous populations from severe influenza disease.


  • Organizational Affiliation

    Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen278Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A5H2UYS3 (Homo sapiens)
Explore A0A5H2UYS3 
Go to UniProtKB:  A0A5H2UYS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5H2UYS3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  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
PB2 peptide from influenza, TYQWIIRNW9Influenza A virusMutation(s): 0 
UniProt
Find proteins for P03428 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03428 
Go to UniProtKB:  P03428
Entity Groups  
UniProt GroupP03428
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.295α = 90
b = 87.295β = 90
c = 312.441γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1159272
National Health and Medical Research Council (NHMRC, Australia)Australia1173871

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description