7EJM | pdb_00007ejm

Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein

• PDB DOI: https://doi.org/10.2210/pdb7EJM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human coronavirus 229E
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-04-02 Released: 2022-01-26 
• Deposition Author(s): Murayama, K., Kato-Murayama, M., Shirouzu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

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

• PubMed: 34857854 
• DOI: https://doi.org/10.1038/s42003-021-02885-6
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan.
Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan.
Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan.
Department of Hematology, National Hospital Organization Kumamoto Medical Center, Kumamoto, Japan.
Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan. [e-mail].
Program for Drug Discovery and Medical Technology Platforms (DMP), RIKEN, Yokohama, Japan. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 45.62 kDa 
• Atom Count: 3,655 
• Modeled Residue Count: 386 
• Deposited Residue Count: 396 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	281	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A5H2UYS3 (Homo sapiens) Explore A0A5H2UYS3  Go to UniProtKB:  A0A5H2UYS3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	106	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
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
9-mer peptide from the HCoV spike protein	C	9	Human coronavirus 229E	Mutation(s): 0
UniProt
Find proteins for P15423 (Human coronavirus 229E) Explore P15423  Go to UniProtKB:  P15423

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.946	α = 90
b = 85.586	β = 90
c = 91.091	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Murayama, K., Kato-Murayama, M., Shirouzu, M.

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary