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Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family

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.

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Fig. 1: Structure of the PVX coat protein.
Fig. 2: Cryo-EM structure of PVX virus at near-atomic resolution.
Fig. 3: Interactions between CP units.
Fig. 4: Qualitative electrostatic surface of 13 units (approximately 1.5 turns) of the PVX virion.
Fig. 5: Details of PVX capsid–RNA interactions.
Fig. 6: Progression of virion assembly.

Data availability

Structural data have been deposited in the PDB under accession number 6R7G and at the Electron Microscopy Data Bank (EMDB) under accession number EMD-4740. Raw data have been deposited in the Electron Microscopy Public Image Archive (EMPIAR). All other data generated or analyzed during this study are included in this published article (and its Supplementary information files) or are available from the corresponding author on reasonable request.

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Acknowledgements

We acknowledge the European Synchrotron Radiation Facility for provision of beam time on CM01. We thank G. A. Leonard for support and for critically reading the manuscript.

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A.G. prepared grids, performed data analysis and processing, and carried out structure determination and refinement. E.K. collected images and supervised A.G. during data processing. C.L., C.B. and S.B. provided the purified virus and performed the mutagenesis experiments. S.B. and G.Z. planned the experiment. G.Z. analyzed the structure. All authors contributed to writing of the paper.

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Correspondence to Giuseppe Zanotti.

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Grinzato, A., Kandiah, E., Lico, C. et al. Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family. Nat Chem Biol 16, 564–569 (2020). https://doi.org/10.1038/s41589-020-0502-4

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