9F13 | pdb_00009f13

Crystal structure of HLA-C*12:02 in complex with KAYNVTQAF (KF9), a 9-mer epitope from SARS-CoV-2 Nucleocapsid (N266-274)

• PDB DOI: https://doi.org/10.2210/pdb9F13/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-04-18 Released: 2025-08-06 
• Deposition Author(s): Ahn, Y.M., Maddumage, J.C., Chatzileontiadou, D.S.M., Gras, S.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Molecular basis of potent antiviral HLA-C-restricted CD8 + T cell response to an immunodominant SARS-CoV-2 nucleocapsid epitope.

Goto, Y., Ahn, Y.M., Toyoda, M., Hamana, H., Jin, Y., Aritsu, Y., Nakama, T., Tajima, Y., Maddumage, J.C., Li, H., Kitamatsu, M., Kishi, H., Yonekawa, A., Jayasinghe, D., Shimono, N., Nagasaki, Y., Minami, R., Toya, T., Sekiya, N., Tomita, Y., Chatzileontiadou, D.S.M., Nakata, H., Nakagawa, S., Sakagami, T., Ueno, T., Gras, S., Motozono, C.

(2025) Nat Commun 16: 8062-8062

• PubMed: 40877317 
• DOI: https://doi.org/10.1038/s41467-025-63288-3
• Primary Citation Related Structures: 
  9F13, 9HLJ


• PubMed Abstract: 
  

  The emergence of SARS-CoV-2 Variants of Concern (VOC) is a major clinical threat; however, VOC remain susceptible to cytotoxic T lymphocyte (CTL) recognition. Therefore, it is crucial to identify potent CTL responses targeting conserved epitopes across VOCs. Here, we demonstrate that the nucleocapsid (N) protein induces efficient CTL responses in early pandemic COVID-19 convalescent donors. In the context of the HLA-A24-B52-C12 haplotype, prevalent in Japan, the KF9 peptide (N _266-274 : KAYNVTQAF) is immunodominant and restricted by HLA-C*12:02. KF9-specific T cells are cytotoxic and suppress viral replication of both the ancestral and multiple VOC SARS-CoV-2. KF9-specific CD8 ⁺ T cells maintain effector memory and terminally differentiated phenotypes for 12 months post-infection and proliferate rapidly upon recall. We also determine the structure of a TCR in the context of the HLA-C*12:02-KF9 complex, providing a prototype for the interaction of HLA-C with viral peptides. Surprisingly, despite the TCR's high affinity, the CDR3β loop almost lacks contact with the KF9 peptide. These findings highlight the importance of conserved epitopes and the role of HLA-C molecules in controlling SARS-CoV-2 VOC.

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Organizational Affiliation: 
• Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, 8600811, Japan.
Department of Respiratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, 8608556, Japan.
Immunity and Infection program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, VIC, 3086, Australia.
Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, 3086, Australia.
Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, 9300194, Japan.
Department of Applied Chemistry, Faculty of Science and Engineering, Kindai University, Osaka, 577-8502, Japan.
Center for the Study of Global Infection, Kyushu University Hospital, Kyushu University, Fukuoka, 8128582, Japan.
Division of Infectious Diseases, Clinical Research Institute, National Hospitalization Organization, Kyushu Medical Center, Fukuoka, 8108563, Japan.
Internal Medicine, Clinical Research Institute, National Hospital Organization, Kyushu Medical Center, Fukuoka, 8108563, Japan.
Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, 1138677, Japan.
Department of Infection Prevention and Control, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, 1138677, Japan.
Department of Infectious Disease Emergency Preparedness, Institute of Science Tokyo, Tokyo, 1138510, Japan.
Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto University Hospital, Kumamoto, 8608556, Japan.
Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, 2591193, Japan.
Immunity and Infection program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, VIC, 3086, Australia. [e-mail].
Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, 3086, Australia. [e-mail].
Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia. [e-mail].
Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, 8600811, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.86 kDa 
• Atom Count: 3,426 
• Modeled Residue Count: 385 
• Deposited Residue Count: 475 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen C alpha chain	A	366	Homo sapiens	Mutation(s): 0  Gene Names: HLA-C, HLA-Cw
UniProt
Find proteins for Q546I6 (Homo sapiens) Explore Q546I6  Go to UniProtKB:  Q546I6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	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
Nucleoprotein	C	9	Severe acute respiratory syndrome coronavirus 2	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: 1.61 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.102	α = 90
b = 77.123	β = 100.201
c = 83.11	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Ahn, Y.M., Maddumage, J.C., Chatzileontiadou, D.S.M., Gras, S.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Database references