6M3M

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.258 

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This is version 1.4 of the entry. See complete history. 


Literature

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:  
    6M3M

  • 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 ...

    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: 

    Department of Experimental Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoprotein
A, B, C, D
136Severe 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement

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