8TUB

HLA B7:02 with HPNGYKSLSTL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CD8 + T-cell responses towards conserved influenza B virus epitopes across anatomical sites and age.

Menon, T.Illing, P.T.Chaurasia, P.McQuilten, H.A.Shepherd, C.Rowntree, L.C.Petersen, J.Littler, D.R.Khuu, G.Huang, Z.Allen, L.F.Rockman, S.Crowe, J.Flanagan, K.L.Wakim, L.M.Nguyen, T.H.O.Mifsud, N.A.Rossjohn, J.Purcell, A.W.van de Sandt, C.E.Kedzierska, K.

(2024) Nat Commun 15: 3387-3387

  • DOI: https://doi.org/10.1038/s41467-024-47576-y
  • Primary Citation of Related Structures:  
    8TUB, 8TUH

  • PubMed Abstract: 

    Influenza B viruses (IBVs) cause substantive morbidity and mortality, and yet immunity towards IBVs remains understudied. CD8 + T-cells provide broadly cross-reactive immunity and alleviate disease severity by recognizing conserved epitopes. Despite the IBV burden, only 18 IBV-specific T-cell epitopes restricted by 5 HLAs have been identified currently. A broader array of conserved IBV T-cell epitopes is needed to develop effective cross-reactive T-cell based IBV vaccines. Here we identify 9 highly conserved IBV CD8 + T-cell epitopes restricted to HLA-B*07:02, HLA-B*08:01 and HLA-B*35:01. Memory IBV-specific tetramer + CD8 + T-cells are present within blood and tissues. Frequencies of IBV-specific CD8 + T-cells decline with age, but maintain a central memory phenotype. HLA-B*07:02 and HLA-B*08:01-restricted NP 30-38 epitope-specific T-cells have distinct T-cell receptor repertoires. We provide structural basis for the IBV HLA-B*07:02-restricted NS1 196-206 (11-mer) and HLA-B*07:02-restricted NP 30-38 epitope presentation. Our study increases the number of IBV CD8 + T-cell epitopes, and defines IBV-specific CD8 + T-cells at cellular and molecular levels, across tissues and age.


  • 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
Beta-2-microglobulinA,
D [auth B],
G [auth E],
J [auth I]
99Homo 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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-7 alpha chainB [auth F],
E [auth C],
H [auth G],
K [auth J]
275Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HIS-PRO-ASN-GLY-TYR-LYS-SER-LEU-SER-THR-LEUC [auth Q],
F [auth D],
I [auth H],
L [auth K]
11Influenza B virusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.211α = 97.54
b = 90.668β = 93.83
c = 104.563γ = 90.23
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references