5IP3

Tomato spotted wilt tospovirus nucleocapsid protein-ssDNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.

Komoda, K.Narita, M.Yamashita, K.Tanaka, I.Yao, M.

(2017) J Virol 91

  • DOI: 10.1128/JVI.01002-17
  • Primary Citation of Related Structures:  
    5IP1, 5IP3, 5IP2

  • PubMed Abstract: 
  • Tomato spotted wilt virus (TSWV), belonging to the genus Tospovirus of the family Bunyaviridae , causes significant economic damage to several vegetables and ornamental plants worldwide. Similar to those of all other negativ ...

    Tomato spotted wilt virus (TSWV), belonging to the genus Tospovirus of the family Bunyaviridae , causes significant economic damage to several vegetables and ornamental plants worldwide. Similar to those of all other negative-strand RNA viruses, the nucleocapsid (N) protein plays very important roles in its viral life cycle. N proteins protect genomic RNAs by encapsidation and form a viral ribonucleoprotein complex (vRNP) with some RNA-dependent RNA polymerases. Here we show the crystal structure of the N protein from TSWV. Protomers of TSWV N proteins consist of three parts: the N arm, C arm, and core domain. Unlike N proteins of other negative-strand RNA viruses, the TSWV N protein forms an asymmetric trimeric ring. To form the trimeric ring, the N and C arms of the N protein interact with the core domains of two adjacent N proteins. By solving the crystal structures of the TSWV N protein with nucleic acids, we showed that an inner cleft of the asymmetric trimeric ring is an RNA-binding site. These characteristics are similar to those of N proteins of other viruses of the family Bunyaviridae Based on these observations, we discuss possibilities of a TSWV encapsidation model. IMPORTANCE Tospoviruses cause significant crop losses throughout the world. Particularly, TSWV has an extremely wide host range (>1,000 plant species, including dicots and monocots), and worldwide losses are estimated to be in excess of $1 billion annually. Despite such importance, no proteins of tospoviruses have been elucidated so far. Among TSWV-encoded proteins, the N protein is required for assembling the viral genomic RNA into the viral ribonucleoprotein (vRNP), which is involved in various steps of the life cycle of these viruses, such as RNA replication, virus particle formation, and cell-to-cell movement. This study revealed the structure of the N protein, with or without nucleic acids, of TSWV as the first virus of the genus Tospovirus , so it completed our view of the N proteins of the family Bunyaviridae .


    Organizational Affiliation

    Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinABC279Tomato spotted wilt tospovirusMutation(s): 0 
Gene Names: N
Find proteins for F4ZD19 (Tomato spotted wilt virus)
Explore F4ZD19 
Go to UniProtKB:  F4ZD19
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*TP*TP*TP*T)-3')D5synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')E7synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')F6synthetic construct
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 3.00 Å
        • R-Value Free: 0.291 
        • R-Value Work: 0.251 
        • R-Value Observed: 0.253 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 68.94α = 90
        b = 86.457β = 112.1
        c = 66.322γ = 90
        Software Package:
        Software NamePurpose
        XDSdata processing
        PHENIXrefinement
        PDB_EXTRACTdata extraction

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2017-03-22
          Type: Initial release
        • Version 2.0: 2017-06-14
          Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence
        • Version 2.1: 2018-03-21
          Changes: Database references