8RNH

Crystal structure of HLA B*18:01 in complex with EEIEITTHF, an 9-mer epitope from Influenza A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Literature

Characterisation of novel influenza-derived HLA-B*18:01-restricted epitopes.

Leong, S.L.Murdolo, L.Maddumage, J.C.Koutsakos, M.Kedzierska, K.Purcell, A.W.Gras, S.Grant, E.J.

(2024) Clin Transl Immunology 13: e1509-e1509

  • DOI: https://doi.org/10.1002/cti2.1509
  • Primary Citation of Related Structures:  
    8RNH, 8ROO, 8ROP

  • PubMed Abstract: 

    Seasonal influenza viruses cause roughly 650 000 deaths annually despite available vaccines. CD8 + T cells typically recognise influenza-derived peptides from internal structural and non-structural influenza proteins and are an attractive avenue for future vaccine design as they could reduce the severity of disease following infection with diverse influenza strains. CD8 + T cells recognise peptides presented by the highly polymorphic Human Leukocyte Antigens class I molecules (HLA-I). Each HLA-I variant has distinct peptide binding preferences, representing a significant obstacle for designing vaccines that elicit CD8 + T cell responses across broad populations. Consequently, the rational design of a CD8 + T cell-mediated vaccine would require the identification of highly immunogenic peptides restricted to a range of different HLA molecules. Here, we assessed the immunogenicity of six recently published novel influenza-derived peptides identified by mass-spectrometry and predicted to bind to the prevalent HLA-B*18:01 molecule. Using CD8 + T cell activation assays and protein biochemistry, we showed that 3/6 of the novel peptides were immunogenic in several HLA-B*18:01 + individuals and confirmed their HLA-B*18:01 restriction. We subsequently compared CD8 + T cell responses towards the previously identified highly immunogenic HLA-B*18:01-restricted NP 219 peptide. Using X-ray crystallography, we solved the first crystal structures of HLA-B*18:01 presenting immunogenic influenza-derived peptides. Finally, we dissected the first TCR repertoires specific for HLA-B*18:01 restricted pathogen-derived peptides, identifying private and restricted repertoires against each of the four peptides. Overall the characterisation of these novel immunogenic peptides provides additional HLA-B*18:01-restricted vaccine targets derived from the Matrix protein 1 and potentially the non-structural protein and the RNA polymerase catalytic subunit of influenza viruses.


  • Organizational Affiliation

    Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS) La Trobe University Bundoora VIC Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen276Homo sapiensMutation(s): 0 
Gene Names: HLA-B
UniProt
Find proteins for S6AU73 (Homo sapiens)
Explore S6AU73 
Go to UniProtKB:  S6AU73
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS6AU73
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitB [auth C]9Influenza A virus (A/Memphis/18/1978(H3N2))Mutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for Q2VNC5 (Influenza A virus (strain A/Memphis/18/1978 H3N2))
Explore Q2VNC5 
Go to UniProtKB:  Q2VNC5
Entity Groups  
UniProt GroupQ2VNC5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinC [auth B]100Homo 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.75α = 90
b = 81.627β = 90
c = 110.556γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references