Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form

Experimental Data Snapshot

  • Resolution: 1.42 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

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This is version 1.5 of the entry. See complete history


Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.

Ye, Q.West, A.M.V.Silletti, S.Corbett, K.D.

(2020) Protein Sci 29: 1890-1901

  • DOI: https://doi.org/10.1002/pro.3909
  • Primary Citation of Related Structures:  
    6WZO, 6WZQ

  • PubMed Abstract: 

    The COVID-2019 pandemic is the most severe acute public health threat of the twenty-first century. To properly address this crisis with both robust testing and novel treatments, we require a deep understanding of the life cycle of the causative agent, the SARS-CoV-2 coronavirus. Here, we examine the architecture and self-assembly properties of the SARS-CoV-2 nucleocapsid protein, which packages viral RNA into new virions. We determined a 1.4 Å resolution crystal structure of this protein's N2b domain, revealing a compact, intertwined dimer similar to that of related coronaviruses including SARS-CoV. While the N2b domain forms a dimer in solution, addition of the C-terminal spacer B/N3 domain mediates formation of a homotetramer. Using hydrogen-deuterium exchange mass spectrometry, we find evidence that at least part of this putatively disordered domain is structured, potentially forming an α-helix that self-associates and cooperates with the N2b domain to mediate tetramer formation. Finally, we map the locations of amino acid substitutions in the N protein from over 38,000 SARS-CoV-2 genome sequences. We find that these substitutions are strongly clustered in the protein's N2a linker domain, and that substitutions within the N1b and N2b domains cluster away from their functional RNA binding and dimerization interfaces. Overall, this work reveals the architecture and self-assembly properties of a key protein in the SARS-CoV-2 life cycle, with implications for both drug design and antibody-based testing.

  • Organizational Affiliation

    Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
121Severe 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

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.718α = 106.499
b = 50.061β = 90.094
c = 69.337γ = 97.145
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Database references
  • Version 1.3: 2020-09-09
    Changes: Database references
  • Version 1.4: 2021-04-07
    Changes: Database references
  • Version 1.5: 2023-10-18
    Changes: Data collection, Database references, Refinement description