7UXX

Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.

Mercaldi, G.F., Bezerra, E.H.S., Batista, F.A.H., Tonoli, C.C.C., Soprano, A.S., Shimizu, J.F., Nagai, A., da Silva, J.C., Filho, H.V.R., do Nascimento Faria, J., da Cunha, M.G., Zeri, A.C.M., Nascimento, A.F.Z., Proenca-Modena, J.L., Bajgelman, M.C., Rocco, S.A., Lopes-de-Oliveira, P.S., Cordeiro, A.T., Bruder, M., Marques, R.E., Sforca, M.L., Franchini, K.G., Benedetti, C.E., Figueira, A.C.M., Trivella, D.B.B.

(2022) Sci Rep 12: 18500-18500

  • DOI: 10.1038/s41598-022-22576-4
  • Primary Citation of Related Structures:  
    7UXX, 7UXZ

  • PubMed Abstract: 

    • The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal ...

    The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal. Several phenolic compounds, including L-chicoric acid (CA), were identified as high-affinity N-protein ligands. The binding of CA to the N protein was confirmed by isothermal titration calorimetry, 1 H-STD and 15 N-HSQC NMR, and by the crystal structure of CA bound to the N protein C-terminal domain (CTD), further revealing a new modulatory site in the SARS-CoV-2 N protein. Moreover, CA reduced SARS-CoV-2 replication in cell cultures. These data thus open venues for the development of new antivirals targeting the N protein, an essential and yet underexplored coronavirus target.

    Organizational Affiliation: 

    Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-100, Brazil. daniela.trivella@lnbio.cnpem.br.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoprotein114Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: N
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
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.615α = 90
b = 119.75β = 90
c = 128.568γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentBrazil01.20.0003.00
Other governmentBrazil--
Other governmentBrazil--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references