4CSF

Structural insights into Toscana virus RNA encapsidation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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:  
    4CSF, 4CSG

  • 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 nucleoprotein N to form the ribonucleoprotein complex (RNP) ...

    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 Freie Universität Berlin, Biochemistry, Takustrasse 6, 14195 Berlin, Germany oliver.daumke@mdc-berlin.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOPROTEIN
A, B, D, F, G, H, I, J
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
UniProt
Find proteins for P21701 (Toscana virus)
Explore P21701 
Go to UniProtKB:  P21701
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOPROTEINC, X253Toscana virusMutation(s): 0 
Gene Names: N
UniProt
Find proteins for P21701 (Toscana virus)
Explore P21701 
Go to UniProtKB:  P21701
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOPROTEINE253Toscana virusMutation(s): 0 
Gene Names: N
UniProt
Find proteins for P21701 (Toscana virus)
Explore P21701 
Go to UniProtKB:  P21701
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*GP*UP*GP*UP*UP*UP*CP*UP)-3')9synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.240 
    • R-Value Work: 0.203 
    • R-Value Observed: 0.205 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 98.777α = 82.1
    b = 127.837β = 79.75
    c = 170.467γ = 74.49
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XDSdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

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

    Revision History  (Full details and data files)

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