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.
Your institute does not have access to this article
Subscribe to Nature+
Get immediate online access to the entire Nature family of 50+ journals
Subscribe to Journal
Get full journal access for 1 year
only $9.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
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.
Adams, M. J. et al. Virology division news: the new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch. Virol. 149, 1045–1060 (2004).
Huisman, M. J., Linthorst, H. J., Bol, J. F. & Cornelissen, J. C. The complete nucleotide sequence of potato virus X and its homologies at the amino acid level with various plus-stranded RNA viruses. J. Gen. Virol. 69, 1789–1798 (1988).
Skryabin, K. G. et al. Conserved and variable elements in RNA genomes of potexviruses. FEBS Lett. 240, 33–40 (1988).
Kendall, A. et al. Structure of flexible filamentous plant viruses. J. Virol. 82, 9546–9554 (2008).
Scholthof, K.-B. G. et al. Top 10 plant viruses in molecular plant pathology. Mol. Plant Pathol. 12, 938–954 (2011).
Verchot-Lubicz, J., Ye, C. M. C.-M. & Bamunusinghe, D. Molecular biology of potexviruses: recent advances. J. Gen. Virol. 88, 1643–1655 (2007).
Röder, J., Dickmeis, C. & Commandeur, U. Small, smaller, nano: new applications for potato virus X in Nanotechnology. Front. Plant Sci. 10, 1–17 (2019).
Lico, C., Schoubben, A., Baschieri, S., Blasi, P. & Santi, L. Nanoparticles in biomedicine: new insights from plant viruses. Curr. Med. Chem. 20, 3471–3487 (2013).
Lico, C., Benvenuto, E. & Baschieri, S. The two-faced potato virus X: from plant pathogen to smart nanoparticle. Front. Plant Sci. 6, 1009 (2015).
Baratova, L. A. et al. The organization of potato virus X coat proteins in virus particles studied by tritium planigraphy and model building. Virology 188, 175–180 (1992).
Lukashina, E. et al. Tritium planigraphy study of structural alterations in the coat protein of Potato virus X induced by binding of its triple gene block 1 protein to virions. FEBS J. 276, 7006–7015 (2009).
Lukashina, E. et al. Analysis of the role of the coat protein N-terminal segment in potato virus X virion stability and functional activity. Mol. Plant Pathol. 13, 38–45 (2012).
Parker, L., Kendall, A. & Stubbs, G. Surface features of potato virus X from fiber diffraction. Virology 300, 291–295 (2002).
DiMaio, F. et al. The molecular basis for flexibility in the flexible filamentous plant viruses. Nat. Struct. Mol. Biol. 22, 642–644 (2015).
Agirrezabala, X. et al. The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses. eLife 4, e11795 (2015).
Zamora, M. et al. Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses. Sci. Adv. 3, eaao2182 (2017).
Kendall, A. et al. A common structure for the potexviruses. Virology 436, 173–178 (2013).
Valle, M. Structural homology between nucleoproteins of ssRNA viruses. Sub-Cell. Biochem. 88, 129–145 (2018).
Yang, S. et al. Crystal structure of the coat protein of the flexible filamentous papaya mosaic virus. J. Mol. Biol. 422, 263–273 (2012).
Tozzini, A. C., Ek, B., Palva, E. T. & Hopp, H. E. Potato virus X coat protein: a glycoprotein. Virology 202, 651–658 (1994).
Baratova, L. A. et al. N-Terminal segment of potato virus X coat protein subunits is glycosylated and mediates formation of a bound water shell on the virion surface. Eur. J. Biochem. 271, 3136–3145 (2004).
Chapman, S., Hills, G., Watts, J. & Baulcombe, D. Mutational analysis of the coat protein gene of potato virus X: effects on virion morphology and viral pathogenicity. Virology 191, 223–230 (1992).
Betti, C. et al. Potato virus X movement in Nicotiana benthamiana: new details revealed by chimeric coat protein variants. Mol. Plant Pathol. 13, 198–203 (2012).
Olson, W. K. Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking. Macromolecules 13, 721–728 (1980).
Keating, K. S., Humphris, E. L. & Pyle, A. M. A new way to see RNA. Q. Rev. Biophys. 44, 433–466 (2011).
Kezar, A. et al. Structural basis for the multitasking nature of the potato virus Y coat protein. Sci. Adv. 5, 1–14 (2019).
Kaftanova, A. S., Kiselev, N. A., Novikov, V. K. & Atabekov, J. G. Structure of products of protein reassembly and reconstruction of potato virus X. Virology 65, 283–287 (1975).
Kwon, S.-J. et al. cis-Acting sequences required for coat protein binding and in vitro assembly of potato virus X. Virology 334, 83–97 (2005).
Park, M.-R., Kwon, S.-J., Choi, H.-S., Hemenway, C. L. & Kim, K.-H. Mutations that alter a repeated ACCA element located at the 5′ end of the Potato virus X genome affect RNA accumulation. Virology 378, 133–141 (2008).
Atabekov, J. G. et al. Translational activation of encapsidated potato virus X RNA by coat protein phosphorylation. Virology 286, 466–474 (2001).
Kozlovsky, S. V. et al. Effect of the N-terminal domain of the coat protein of potato virus X on the structure of viral particles. Dokl. Biochem. Biophys. 391, 189–191 (2003).
Le, D. H. T., Lee, K. L., Shukla, S., Commandeur, U. & Steinmetz, N. F. Potato virus X, a filamentous plant viral nanoparticle for doxorubicin delivery in cancer therapy. Nanoscale 9, 2348–2357 (2017).
Lico, C. et al. Plant-produced potato virus X chimeric particles displaying an influenza virus-derived peptide activate specific CD8+ T cells in mice. Vaccine 27, 5069–5076 (2009).
Blandino, A. et al. In vitro and in vivo toxicity evaluation of plant virus nanocarriers. Colloids Surf. B Biointerfaces 129, 130–136 (2015).
Lico, C. et al. A biodistribution study of two differently shaped plant virus nanoparticles reveals new peculiar traits. Colloids Surf. B Biointerfaces 148, 431–439 (2016).
Lico, C. et al. Peptide display on Potato virus X: molecular features of the coat protein-fused peptide affecting cell-to-cell and phloem movement of chimeric virus particles. J. Gen. Virol. 87, 3103–3112 (2006).
Vaculik, P. et al. Potato virus X displaying the E7 peptide derived from human papillomavirus type 16: a novel position for epitope presentation. Plant Cell, Tissue Organ Cult. 120, 671–680 (2015).
Cerovska, N. et al. Transient expression of Human papillomavirus type 16 L2 epitope fused to N- and C-terminus of coat protein of Potato virus X in plants. J. Biosci. 37, 125–133 (2012).
Hoffmeisterova, H., Moravec, T., Plchova, H., Folwarczna, J. & Cerovska, N. The influence of the N- and C- terminal modifications of Potato virus X coat protein on virus properties. Biol. Plant. 56, 775–779 (2012).
Kandiah, E. et al. CM01: a facility for cryo-electron microscopy at the European Synchrotron. Acta Crystallogr. D 75, 528–535 (2019).
Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10, 584–590 (2013).
Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
He, S. & Scheres, S. H. W. Helical reconstruction in RELION. J. Struct. Biol. 198, 163–176 (2017).
Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014).
Bienert, S. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Afonine, P. V. et al. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr. D 74, 814–840 (2018).
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.
The authors declare no competing interests.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
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