Structure of Nora virus at 2.7\xa0\xc5 resolution and implications for receptor binding, capsid stability and taxonomy

Pasi Laurinmäki,Dan Hultmark,Jens-Ola Ekström,Pezhman Mohammadi,Shabih Shakeel,Sarah J Butcher

doi:10.1038/s41598-020-76613-1

Abstract

Nora virus, a virus of Drosophila, encapsidates one of the largest single-stranded RNA virus genomes known. Its taxonomic affinity is uncertain as it has a picornavirus-like cassette of enzymes for virus replication, but the capsid structure was at the time for genome publication unknown. By solving the structure of the virus, and through sequence comparison, we clear up this taxonomic ambiguity in the invertebrate RNA virosphere. Despite the lack of detectable similarity in the amino acid sequences, the 2.7 Å resolution cryoEM map showed Nora virus to have T = 1 symmetry with the characteristic capsid protein β-barrels found in all the viruses in the Picornavirales order. Strikingly, α-helical bundles formed from the extended C-termini of capsid protein VP4B and VP4C protrude from the capsid surface. They are similar to signalling molecule folds and implicated in virus entry. Unlike other viruses of Picornavirales, no intra-pentamer stabilizing annulus was seen, instead the intra-pentamer stability comes from the interaction of VP4C and VP4B N-termini. Finally, intertwining of the N-termini of two-fold symmetry-related VP4A capsid proteins and RNA, provides inter-pentamer stability. Based on its distinct structural elements and the genetic distance to other picorna-like viruses we propose that Nora virus, and a small group of related viruses, should have its own family within the order Picornavirales.

Highlights

Nora virus is a positive-sense, single-stranded RNA virus infecting different Drosophila species including Drosophila melanogaster and Drosophila simulans[1]
The models of capsid proteins VP4A, VP4B and VP4C were built de novo to generate an atomic model of Nora virus constrained by the density from the reconstruction (Fig. 2 and Table 1)
The Nora virus capsid asymmetric unit is built from three subunits, a single copy each of VP4A, VP4B and VP4C (Fig. 2c)

Summary

Introduction

Nora virus is a positive-sense, single-stranded RNA virus infecting different Drosophila species including Drosophila melanogaster and Drosophila simulans[1]. We determined a 2.7 Å resolution Nora virus structure using electron cryo-microscopy and single particle image analysis (Fig. 1). The models of capsid proteins VP4A, VP4B and VP4C were built de novo to generate an atomic model of Nora virus constrained by the density from the reconstruction (Fig. 2 and Table 1).

Results

Conclusion