4CSF

Structural insights into Toscana virus RNA encapsidation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights Into RNA Encapsidation and Helical Assembly of the Toscana Virus Nucleoprotein.

Olal, D.Dick, A.Woods, V.L.Liu, T.Li, S.Devignot, S.Weber, F.Saphire, E.O.Daumke, O.

(2014) Nucleic Acids Res. 42: 6025

  • DOI: 10.1093/nar/gku229
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Toscana virus is an emerging bunyavirus in Mediterranean Europe where it accounts for 80% of pediatric meningitis cases during the summer. The negative-strand ribonucleic acid (RNA) genome of the virus is wrapped around the virally encoded nucleoprot ...

    Toscana virus is an emerging bunyavirus in Mediterranean Europe where it accounts for 80% of pediatric meningitis cases during the summer. The negative-strand ribonucleic acid (RNA) genome of the virus is wrapped around the virally encoded nucleoprotein N to form the ribonucleoprotein complex (RNP). We determined crystal structures of hexameric N alone (apo) and in complex with a nonameric single-stranded RNA. RNA is sequestered in a sequence-independent fashion in a deep groove inside the hexamer. At the junction between two adjacent copies of Ns, RNA binding induced an inter-subunit rotation, which opened the RNA-binding tunnel and created a new assembly interface at the outside of the hexamer. Based on these findings, we suggest a structural model for how binding of RNA to N promotes the formation of helical RNPs, which are a characteristic hallmark of many negative-strand RNA viruses.


    Organizational Affiliation

    Max Delbrück Center for Molecular Medicine, Crystallography, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Crystallography, Robert-Rössle-Strasse 10, 13125 Berlin, Germany Freie Universität Berlin, Biochemistry, Takustrasse 6, 14195 Berlin, Germany oliver.daumke@mdc-berlin.de.,Institute for Virology, Philipps-University Marburg, D-35043 Marburg, Germany.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA.,Max Delbrück Center for Molecular Medicine, Crystallography, Robert-Rössle-Strasse 10, 13125 Berlin, Germany Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA oliver.daumke@mdc-berlin.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPROTEIN
A, B, D, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W
253Toscana virusMutation(s): 0 
Gene Names: N
Find proteins for P21701 (Toscana virus)
Go to UniProtKB:  P21701
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPROTEIN
C, X
253Toscana virusMutation(s): 0 
Gene Names: N
Find proteins for P21701 (Toscana virus)
Go to UniProtKB:  P21701
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPROTEIN
E
253Toscana virusMutation(s): 0 
Gene Names: N
Find proteins for P21701 (Toscana virus)
Go to UniProtKB:  P21701
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*UP*GP*UP*UP*UP*CP*UP)-3')a,c,e,g,i,k,m,o,q,s,u,w9synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 98.777α = 82.10
b = 127.837β = 79.75
c = 170.467γ = 74.49
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-07 
  • Released Date: 2014-04-09 
  • Deposition Author(s): Olal, D., Daumke, O.

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-06-04
    Type: Database references
  • Version 1.2: 2019-10-16
    Type: Data collection, Experimental preparation, Other