7EJL

Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of TCR repertoires in functionally competent cytotoxic T cells cross-reactive to SARS-CoV-2.

Shimizu, K.Iyoda, T.Sanpei, A.Nakazato, H.Okada, M.Ueda, S.Kato-Murayama, M.Murayama, K.Shirouzu, M.Harada, N.Hidaka, M.Fujii, S.I.

(2021) Commun Biol 4: 1365-1365

  • DOI: https://doi.org/10.1038/s42003-021-02885-6
  • Primary Citation of Related Structures:  
    7EJL, 7EJM, 7EJN

  • PubMed Abstract: 

    SARS-CoV-2-specific CD8 + T cells are scarce but detectable in unexposed healthy donors (UHDs). It remains unclear whether pre-existing human coronavirus (HCoV)-specific CD8 + T cells are converted to functionally competent T cells cross-reactive to SARS-CoV-2. Here, we identified the HLA-A24-high binding, immunodominant epitopes in SARS-CoV-2 spike region that can be recognized by seasonal coronavirus-specific CD8 + T cells from HLA-A24 + UHDs. Cross-reactive CD8 + T cells were clearly reduced in patients with hematological malignancy, who are usually immunosuppressed, compared to those in UHDs. Furthermore, we showed that CD8 + T cells in response to a selected dominant epitope display multifunctionality and cross-functionality across HCoVs in HLA-A24 + donors. Cross-reactivity of T-cell receptors isolated from them exhibited selective diversity at the single-cell level. Taken together, when stimulated well by immunodominant epitopes, selective pre-existing CD8 + T cells with high functional avidity may be cross-reactive against SARS-CoV-2.


  • Organizational Affiliation

    Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen281Homo 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-microglobulin106Homo 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
9-mer peptide from the HCoV spike protein9Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
UniProt GroupP0DTC2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.717α = 90
b = 85.465β = 90
c = 91.373γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary