SNAP output for PDB entry 6r7g [SNAP web server]

PDB-id

6r7g; SNAP-derived features in text and JSON formats; DNAproDB

Class

virus

Method

cryo-EM (2.2 Å)

Summary

Atomic structure of potato virus x, the prototype of the alphaflexiviridae family

Reference

Grinzato A, Kandiah E, Lico C, Betti C, Baschieri S, Zanotti G (2020): "Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family." Nat.Chem.Biol., 16, 564-569. doi: 10.1038/s41589-020-0502-4.

Abstract

Potato virus X (PVX) is a positive-sense single-stranded RNA (ssRNA) filamentous plant virus belonging to the Alphaflexiviridae family, considered in recent years as a tool for nanotechnology applications. We present the cryo-electron microscopy structure of the PVX particle at a resolution of 2.2 Å. The well-defined density of the coat proteins and of the genomic RNA allowed a detailed analysis of protein-RNA interactions, including those mediated by solvent molecules. The particle is formed by repeated segments made of 8.8 coat proteins, forming a left-handed helical structure. The RNA runs in an internal crevice along the virion, packaged in 5-nucleotide repeats in which the first four bases are stacked in the classical way, while the fifth is rotated and nearly perpendicular. The resolution of the structure described here suggests a mechanism for the virion assembly and potentially provides a platform for the rational design of antiviral compounds and for the use of PVX in nanotechnology.