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.

• PDB DOI: https://doi.org/10.2210/pdb7WKJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-01-10 Released: 2022-03-02 
• Deposition Author(s): Zhang, J., Lu, D., Li, M., Liu, M.S., Yao, S.J., Zhan, J.B., Liu, J., Gao, G.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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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 

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

• PubMed: 35186375 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.52 kDa 
• Atom Count: 3,518 
• Modelled Residue Count: 382 
• Deposited Residue Count: 382 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A6M6CC39 (Homo sapiens) Explore A0A6M6CC39  Go to UniProtKB:  A0A6M6CC39

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-THR-PHE-PRO-PRO-THR-GLU-PRO-LYS	C	9	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

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 = 43.984	α = 90
b = 81.902	β = 90
c = 116.839	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
REFMAC	refinement
CNS	phasing
PHASES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Zhang, J., Lu, D., Li, M., Liu, M.S., Yao, S.J., Zhan, J.B., Liu, J., Gao, G.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• 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