Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.283 

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This is version 1.2 of the entry. See complete history


Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain.

Sarkar, S.Runge, B.Russell, R.W.Movellan, K.T.Calero, D.Zeinalilathori, S.Quinn, C.M.Lu, M.Calero, G.Gronenborn, A.M.Polenova, T.

(2022) J Am Chem Soc 144: 10543-10555

  • DOI: https://doi.org/10.1021/jacs.2c03320
  • Primary Citation of Related Structures:  
    7SD4, 7UW3

  • PubMed Abstract: 

    The nucleocapsid (N) protein is one of the four structural proteins of the SARS-CoV-2 virus and plays a crucial role in viral genome organization and, hence, replication and pathogenicity. The N-terminal domain (N NTD ) binds to the genomic RNA and thus comprises a potential target for inhibitor and vaccine development. We determined the atomic-resolution structure of crystalline N NTD by integrating solid-state magic angle spinning (MAS) NMR and X-ray diffraction. Our combined approach provides atomic details of protein packing interfaces as well as information about flexible regions as the N- and C-termini and the functionally important RNA binding, β-hairpin loop. In addition, ultrafast (100 kHz) MAS 1 H-detected experiments permitted the assignment of side-chain proton chemical shifts not available by other means. The present structure offers guidance for designing therapeutic interventions against the SARS-CoV-2 infection.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
136Severe acute respiratory syndrome coronavirusMutation(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: 1.70 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.283 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.943α = 90
b = 93.066β = 90
c = 96.82γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2023-05-10 
  • Deposition Author(s): Calero, G.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM082251-11

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description