8YZR | pdb_00008yzr

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYLYRLL(EG.5.1)

• PDB DOI: https://doi.org/10.2210/pdb8YZR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-04-08 Released: 2025-01-29 
• Deposition Author(s): Min, L., Liu, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.262 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.

Tian, J., Shang, B., Zhang, J., Guo, Y., Li, M., Hu, Y., Bai, D., She, J., Han, Y., Guo, P., Huang, M., Wang, Y., Liu, M., Zhang, J., Ye, B., Guo, Y., Yang, M., Lin, Y., Zhang, T., Sun, X., Yuan, X., Zhang, D., Xu, Z., Chai, Y., Qi, J., Liu, K., Tan, S., Zhao, Y., Zhou, J., Song, R., Gao, G.F., Liu, J.

(2025) Nat Immunol 26: 265-278

• PubMed: 39875585 
• DOI: https://doi.org/10.1038/s41590-024-02051-0
• Primary Citation of Related Structures:  
  8YZR, 8YZW, 8YZZ, 8Z05, 8Z06, 8Z07, 8Z08


• PubMed Abstract: 
  

  Although antibody escape is observed in emerging severe acute respiratory syndrome coronavirus 2 variants, T cell escape, especially after the global circulation of BA.2.86/JN.1, is unexplored. Here we demonstrate that T cell evasion exists in epitope hotspots spanning BA.2.86/JN.1 mutations. The newly emerging Q229K at this conserved nucleocapsid protein site impairs HLA-A2 epitope hotspot recognition. The association between HLA-A24 convalescents and T cell immune escape points to the spike (S) protein epitope S _448-456 NYNYLYRLF, with multiple mutations from Delta to JN.1, including L452Q, L452R, F456L, N450D and L452W, and N450D, L452W and L455S. A cliff drop of immune responses was observed for S _448-456 NYNYRYRLF (Delta/BA.5.2) and S _448-456 NYDYWYRSF (JN.1), but with immune preservation of S _448-456 NYDYWYRLF (BA.2.86). Structural analyses showed that hydrophobicity exposure determines the pronounced escape of L452R and L455S mutants, which was further confirmed by T cell receptor binding. This study highlights the characteristics and molecular mechanisms of the T cell immune escape for JN.1 and provides new insights into understanding the dominant circulation of variants, from the viewpoint of cytotoxic T cell evasion.

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Organizational Affiliation: 
• National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China.
School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, China.
Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, China.
Beijing Ditan Hospital, Capital Medical University, Beijing, China.
Beijing Institute of Infectious Diseases, Beijing, China.
Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [e-mail].
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [e-mail].
Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China. [e-mail].
The Fifth Hospital of Shijiazhuang, Shijiazhuang, China. [e-mail].
Beijing Ditan Hospital, Capital Medical University, Beijing, China. [e-mail].
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [e-mail].
School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, China. [e-mail].
Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. [e-mail].
The D. H. Chen School of Universal Health, Zhejiang University, Hangzhou, China. [e-mail].
National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [e-mail].
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. [e-mail].
School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China. [e-mail].
Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China. [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: 44.53 kDa 
• Atom Count: 3,424 
• Modeled 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 A0A143Y4R2 (Homo sapiens) Explore A0A143Y4R2  Go to UniProtKB:  A0A143Y4R2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	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
Spike protein S1	C [auth E]	9	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.262 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.672	α = 90
b = 65.388	β = 90.42
c = 50.311	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Min, L., Liu, J.

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

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release
  
• Version 1.1: 2025-05-28
  Changes: Database references, Structure summary