9J4T | pdb_00009j4t

Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors

• PDB DOI: https://doi.org/10.2210/pdb9J4T/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-10 Released: 2025-08-13 
• Deposition Author(s): Yuan, P., Wu, D.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.232 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Models: experimental

Literature

Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors

Yuan, P., Wu, D.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 95.62 kDa 
• Atom Count: 7,308 
• Modeled Residue Count: 817 
• Deposited Residue Count: 834 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
PHAROS:  P01889 GTEx:  ENSG00000234745

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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SPR epitope specific TCR CLB1 ALPHA	D	205	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SPR epitope specific TCR CLB1 BETA	E	244	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.232 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.105	α = 90
b = 102.725	β = 90
c = 160.147	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Yuan, P., Wu, D.C.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32270995
National Natural Science Foundation of China (NSFC)	China	32100985

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release