Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.258 

Starting Model: experimental
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Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites.

Kang, S.Yang, M.Hong, Z.Zhang, L.Huang, Z.Chen, X.He, S.Zhou, Z.Zhou, Z.Chen, Q.Yan, Y.Zhang, C.Shan, H.Chen, S.

(2020) Acta Pharm Sin B 10: 1228-1238

  • DOI: https://doi.org/10.1016/j.apsb.2020.04.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. Currently, there is no specific viral protein-targeted therapeutics. Viral nucleocapsid protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid protein remains unclear. Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Although the overall structure is similar as other reported coronavirus nucleocapsid protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA binding pocket alongside the β -sheet core. Complemented by in vitro binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.

  • Organizational Affiliation

    Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
136Severe 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: 2.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.888α = 90
b = 92.685β = 90
c = 97.325γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770801

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Structure summary
  • Version 1.2: 2020-05-27
    Changes: Database references
  • Version 1.3: 2020-09-09
    Changes: Database references
  • Version 1.4: 2021-02-24
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2023-11-29
    Changes: Data collection, Database references, Refinement description