Crystal structure of oligomerization domain of SARS coronavirus nucleocapsid protein.

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 

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Structure of the Sars Coronavirus Nucleocapsid Protein RNA-Binding Dimerization Domain Suggests a Mechanism for Helical Packaging of Viral RNA.

Chen, C.-Y.Chang, C.K.Chang, Y.W.Sue, S.C.Bai, H.I.Riang, L.Hsiao, C.-D.Huang, T.H.

(2007) J Mol Biol 368: 1075

  • DOI: https://doi.org/10.1016/j.jmb.2007.02.069
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Coronavirus nucleocapsid proteins are basic proteins that encapsulate viral genomic RNA to form part of the virus structure. The nucleocapsid protein of SARS-CoV is highly antigenic and associated with several host-cell interactions. Our previous studies using nuclear magnetic resonance revealed the domain organization of the SARS-CoV nucleocapsid protein. RNA has been shown to bind to the N-terminal domain (NTD), although recently the C-terminal half of the protein has also been implicated in RNA binding. Here, we report that the C-terminal domain (CTD), spanning residues 248-365 (NP248-365), had stronger nucleic acid-binding activity than the NTD. To determine the molecular basis of this activity, we have also solved the crystal structure of the NP248-365 region. Residues 248-280 form a positively charged groove similar to that found in the infectious bronchitis virus (IBV) nucleocapsid protein. Furthermore, the positively charged surface area is larger in the SARS-CoV construct than in the IBV. Interactions between residues 248-280 and the rest of the molecule also stabilize the formation of an octamer in the asymmetric unit. Packing of the octamers in the crystal forms two parallel, basic helical grooves, which may be oligonucleotide attachment sites, and suggests a mechanism for helical RNA packaging in the virus.

  • Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H
128SARS coronavirus TW1Mutation(s): 0 
Find proteins for P59595 (Severe acute respiratory syndrome coronavirus)
Explore P59595 
Go to UniProtKB:  P59595
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59595
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.423α = 90
b = 84.203β = 131.18
c = 105.177γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance