SNAP output for PDB entry 5ip2 [SNAP web server]

PDB-id

5ip2; SNAP-derived features in text and JSON formats; DNAproDB

Class

viral protein-RNA

Method

X-ray (3.3 Å)

Summary

Tomato spotted wilt tospovirus nucleocapsid protein-ssrna complex

Reference

Komoda K, Narita M, Yamashita K, Tanaka I, Yao M (2017): "Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus." J. Virol., 91. doi: 10.1128/JVI.01002-17.

Abstract

Tomato spotted wilt virus (TSWV), belonging to the genusTospovirusof the familyBunyaviridae, 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 familyBunyaviridaeBased on these observations, we discuss possibilities of a TSWV encapsidation model.