4LM7

Crystal structure of HCoV-OC43 N-NTD complexed with UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target

Lin, S.Y.Liu, C.L.Chang, Y.M.Zhao, J.Perlman, S.Hou, M.H.

(2014) J.Med.Chem. 57: 2247-2257

  • DOI: 10.1021/jm500089r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Coronaviruses (CoVs) cause numerous diseases, including Middle East respiratory syndrome and severe acute respiratory syndrome, generating significant health-related and economic consequences. CoVs encode the nucleocapsid (N) protein, a major structu ...

    Coronaviruses (CoVs) cause numerous diseases, including Middle East respiratory syndrome and severe acute respiratory syndrome, generating significant health-related and economic consequences. CoVs encode the nucleocapsid (N) protein, a major structural protein that plays multiple roles in the virus replication cycle and forms a ribonucleoprotein complex with the viral RNA through the N protein's N-terminal domain (N-NTD). Using human CoV-OC43 (HCoV-OC43) as a model for CoV, we present the 3D structure of HCoV-OC43 N-NTD complexed with ribonucleoside 5'-monophosphates to identify a distinct ribonucleotide-binding pocket. By targeting this pocket, we identified and developed a new coronavirus N protein inhibitor, N-(6-oxo-5,6-dihydrophenanthridin-2-yl)(N,N-dimethylamino)acetamide hydrochloride (PJ34), using virtual screening; this inhibitor reduced the N protein's RNA-binding affinity and hindered viral replication. We also determined the crystal structure of the N-NTD-PJ34 complex. On the basis of these findings, we propose guidelines for developing new N protein-based antiviral agents that target CoVs.


    Organizational Affiliation

    College of Life Science, ‡Institute of Genomics and Bioinformatics, and §Agriculture Biotechnology Center, National Chung Hsing University , Taichung 40254, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoprotein
A
136Human coronavirus OC43Mutation(s): 0 
Gene Names: N
Find proteins for P33469 (Human coronavirus OC43)
Go to UniProtKB:  P33469
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P

Download SDF File 
Download CCD File 
A
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.225 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 81.940α = 90.00
b = 81.940β = 90.00
c = 42.820γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release