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

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 

Starting Model: experimental
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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein114Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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

Structure Validation

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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
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description