6WZQ

Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P21 form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

  • 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 ...

    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.


    Related Citations: 
    • Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
      Ye, Q., West, A.M.V., Silletti, S., Corbett, K.D.
      (2020) Biorxiv --: --
    • Architecture and self-assembly of the SARS-CoV-2 ucleocapsid protein
      Ye, Q., West, A.M.V., Silletti, S., Corbett, K.D.
      (2020) Protein Sci --: --

    Organizational Affiliation

    Ludwig Institute for Cancer Research, La Jolla, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinA, B, C, D137Severe 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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 10.15785/SBGRID/786 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.146α = 90
b = 43.546β = 94.87
c = 74.233γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2020-05-14 
  • Released Date: 2020-05-27 
  • Deposition Author(s): Ye, Q., Corbett, K.D.

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