7WKJ

A COVID-19 T-cell response detection method based on a newly identified human CD8+ T cell epitope from SARS-CoV-2-Hubei Province, 2021.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A COVID-19 T-Cell Response Detection Method Based on a Newly Identified Human CD8 + T Cell Epitope from SARS-CoV-2 - Hubei Province, China, 2021.

Zhang, J.Lu, D.Li, M.Liu, M.Yao, S.Zhan, J.Liu, W.J.Gao, G.F.

(2022) China CDC Wkly 4: 83-87

  • DOI: https://doi.org/10.46234/ccdcw2021.258
  • Primary Citation of Related Structures:  
    7WKJ

  • PubMed Abstract: 

    Similar to antibody detection, severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2)-specific T-cell response evaluation is also pivotal among the coronavirus disease 2019 (COVID-19) convalescents and the vaccinated populations. Nucleocapsid (N) protein is one of the main structural proteins of SARS-CoV-2 and can trigger T-cell responses in humans. An overlapping peptide pool covering the full length of the N protein was designed, peptides with positive T-cell activating potency in COVID-19 convalescents were screened, and CD8 + T cell epitopes were further identified. The epitope was used to detect the SARS-CoV-2-specific CD8 + T cell responses in COVID-19 convalescents based in intracellular cytokine staining and tetramer staining in flow cytometry. A human leukocyte antigen A (HLA-A)*1101-restricted CD8 + T cell epitope, which could stimulate the production of IFN-γ via peripheral blood mononuclear cells (PBMCs) of the convalescents was defined, and the tetramer generated with this epitope could detect SARS-CoV-2-specific T cells in the PBMCs of the convalescents. The structural investigation eliminated that the epitope was a typical HLA-A*1101-restricted T-cell epitope which was conserved among all the sarbecoviruses. The newly identified SARS-CoV-2-derived T-cell epitope was helpful to detect the cellular immunity against different sarbecoviruses including SARS-CoV and SARS-CoV-2. This study provided an evaluation method and also a peptide candidate for the research and development of T-cell based vaccine for the virus.


  • Organizational Affiliation

    NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen274Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A6M6CC39 (Homo sapiens)
Explore A0A6M6CC39 
Go to UniProtKB:  A0A6M6CC39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M6CC39
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2M
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
LYS-THR-PHE-PRO-PRO-THR-GLU-PRO-LYS9Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups  
UniProt GroupP0DTC9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.984α = 90
b = 81.902β = 90
c = 116.839γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
REFMACrefinement
CNSphasing
PHASESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary