9KN1 | pdb_00009kn1

Crystal structure of SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain(N-NTD) in complex with UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.293 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural insights into nucleocapsid protein variability: Implications for PJ34 efficacy against SARS-CoV-2.

Yamamoto, A.Ito, H.Sakaguchi, T.Higashiura, A.

(2025) Virology 604: 110411-110411

  • DOI: https://doi.org/10.1016/j.virol.2025.110411
  • Primary Citation Related Structures: 
    9KN1

  • PubMed Abstract: 

    Human coronaviruses (HCoVs) include common cold viruses such as HCoV-229E, OC43, NL63 and HKU1 as well as MERS-CoV and SARS-CoV, which cause severe respiratory disease. Recently, SARS-CoV-2 caused a COVID-19 pandemic. The nucleocapsid (N) protein of coronaviruses, which is essential for RNA binding and homodimerization, has a highly conserved structure across viruses. Previous studies revealed that compound PJ34 is an inhibitor of nucleic acid binding to the N-terminal domain (NTD) of the HCoV-OC43 N protein, suggesting that it could block viral replication. However, testing with SARS-CoV-2 showed that PJ34 did not inhibit viral replication. Structural analysis suggests that the substitution of Tyr for Ala at position 50 (corresponding to Tyr63 in OC43), may affect the ability to interact with compounds such as PJ34, explaining its lack of efficacy. These findings underscore the importance of structure-based drug development targeting the N protein, which remains an important therapeutic target in all coronaviruses.


  • Organizational Affiliation
    • Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan. Electronic address: akm@hiroshima-u.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 56.09 kDa 
  • Atom Count: 4,226 
  • Modeled Residue Count: 506 
  • Deposited Residue Count: 506 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein125Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein128Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein127Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein126Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.293 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.753α = 90
b = 92.659β = 90
c = 97.412γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release