4JNG

Schmallenberg virus nucleoprotein-RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of Schmallenberg orthobunyavirus nucleoprotein-RNA complex reveals a novel RNA sequestration mechanism.

Dong, H.H.Li, P.Bottcher, B.Elliott, R.M.Dong, C.J.

(2013) Rna 19: 1129-1136

  • DOI: 10.1261/rna.039057.113

  • PubMed Abstract: 
  • Schmallenberg virus (SBV) is a newly emerged orthobunyavirus (family Bunyaviridae) that has caused severe disease in the offspring of farm animals across Europe. Like all orthobunyaviruses, SBV contains a tripartite negative-sense RNA genome that is ...

    Schmallenberg virus (SBV) is a newly emerged orthobunyavirus (family Bunyaviridae) that has caused severe disease in the offspring of farm animals across Europe. Like all orthobunyaviruses, SBV contains a tripartite negative-sense RNA genome that is encapsidated by the viral nucleocapsid (N) protein in the form of a ribonucleoprotein complex (RNP). We recently reported the three-dimensional structure of SBV N that revealed a novel fold. Here we report the crystal structure of the SBV N protein in complex with a 42-nt-long RNA to 2.16 Å resolution. The complex comprises a tetramer of N that encapsidates the RNA as a cross-shape inside the protein ring structure, with each protomer bound to 11 ribonucleotides. Eight bases are bound in the positively charged cleft between the N- and C-terminal domains of N, and three bases are shielded by the extended N-terminal arm. SBV N appears to sequester RNA using a different mechanism compared with the nucleoproteins of other negative-sense RNA viruses. Furthermore, the structure suggests that RNA binding results in conformational changes of some residues in the RNA-binding cleft and the N- and C-terminal arms. Our results provide new insights into the novel mechanism of RNA encapsidation by orthobunyaviruses.


    Organizational Affiliation

    Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park NR4 7TJ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nucleocapsid protein
A, B, C, D
233Bovine Schmallenberg virusGene Names: N
Find proteins for H2AM13 (Bovine Schmallenberg virus)
Go to UniProtKB:  H2AM13
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (42-MER)L42N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.264 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.350α = 90.00
b = 85.960β = 102.02
c = 77.330γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Experimental preparation