4IDX

hexameric crystal structure of Schmallenberg virus nucleoprotein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.374 
  • R-Value Work: 0.321 
  • R-Value Observed: 0.324 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure of Schmallenberg orthobunyavirus nucleoprotein suggests a novel mechanism of genome encapsidation

Dong, H., Li, P., Elliott, R.M., Dong, C.

(2013) J Virol 87: 5593-5601

  • DOI: 10.1128/JVI.00223-13
  • Primary Citation of Related Structures:  
    4IDU, 4IDX

  • PubMed Abstract: 

    • Schmallenberg virus (SBV), a newly emerged orthobunyavirus (family Bunyaviridae), has spread rapidly across Europe and has caused congenital abnormalities in the offspring of cattle, sheep, and goats. Like other orthobunyaviruses, SBV contains a tripartite negative-sense RNA genome that encodes four structural and two nonstructural proteins ...

    Schmallenberg virus (SBV), a newly emerged orthobunyavirus (family Bunyaviridae), has spread rapidly across Europe and has caused congenital abnormalities in the offspring of cattle, sheep, and goats. Like other orthobunyaviruses, SBV contains a tripartite negative-sense RNA genome that encodes four structural and two nonstructural proteins. The nucleoprotein (N) encapsidates the three viral genomic RNA segments and plays a crucial role in viral RNA transcription and replication. Here we report the crystal structure of the bacterially expressed SBV nucleoprotein to a 3.06-Å resolution. The protomer is composed of two domains (N-terminal and C-terminal domains) with flexible N-terminal and C-terminal arms. The N protein has a novel fold and forms a central positively charged cleft for genomic RNA binding. The nucleoprotein purified under native conditions forms a tetramer, while the nucleoprotein obtained following denaturation and refolding forms a hexamer. Our structural and functional analyses demonstrate that both N-terminal and C-terminal arms are involved in N-N interaction and oligomerization and play an essential role in viral RNA synthesis, suggesting a novel mechanism for viral RNA encapsidation and transcription.

    Organizational Affiliation: 

    Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleocapsid proteinB [auth A],
A [auth B],
C		233Schmallenberg virusMutation(s): 0 
Gene Names: N
UniProt
Find proteins for H2AM13 (Bovine Schmallenberg virus (isolate Bovine/BH80/Germany/2011))
Explore H2AM13 
Go to UniProtKB:  H2AM13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2AM13
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.374 
  • R-Value Work: 0.321 
  • R-Value Observed: 0.324 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.2α = 90
b = 159.2β = 90
c = 157.8γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-12-13 
  • Released Date: 2013-04-24 
    • Deposition Author(s): Dong, H., Dong, C.

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Data collection