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Home›Coefficient of Variation›Cryo-electron microscopy and image classification reveal the existence and structure of the coxsackievirus A6 virion

Cryo-electron microscopy and image classification reveal the existence and structure of the coxsackievirus A6 virion

By Maureen Bellinger
September 2, 2022
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  • Tapparel, C., Siegrist, F., Petty, T. J. & Kaiser, L. Picornavirus and enterovirus diversity with associated human diseases. Infect. Genet. Evol. 14, 282–293 (2013).

    PubMed 
    Article 

    Google Scholar 

  • Rhoades, R. E., Tabor-Godwin, J. M., Tsueng, G. & Feuer, R. Enterovirus infections of the central nervous system. Virology 411, 288–305 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Hughes, L. E. & Ryan, M. D. in Encyclopedia of Virology (Third Edition) (eds Mahy, B. W. J. & Van Regenmortel, M. H. V.) (Academic Press, 2008).

  • Bian, L. et al. Coxsackievirus A6: a new emerging pathogen causing hand, foot and mouth disease outbreaks worldwide. Expert Rev. Anti Infect. Ther. 13, 1061–1071 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Ang, L. W. et al. Seroepidemiology of coxsackievirus A6, coxsackievirus A16, and enterovirus 71 infections among children and adolescents in Singapore, 2008-2010. PLoS ONE 10, e0127999 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Österback, R. et al. Coxsackievirus A6 and hand, foot, and mouth disease, Finland. Emerg. Infect. Dis. 15, 1485–1488 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Fujimoto, T. et al. Hand, foot, and mouth disease caused by coxsackievirus A6, Japan, 2011. Emerg. Infect. Dis. 18, 337–339 (2012).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Fujimoto, T. [Hand-foot-and-mouth disease, aseptic meningitis, and encephalitis caused by enterovirus]. Brain Nerve 70, 121–131 (2018).

  • Li, Y. et al. Emerging enteroviruses causing hand, foot and mouth disease, China, 2010-2016. Emerg. Infect. Dis. 24, 1902–1906 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Gao, L. et al. Spectrum of enterovirus serotypes causing uncomplicated hand, foot, and mouth disease and enteroviral diagnostic yield of different clinical samples. Clin. Infect. Dis. 67, 1729–1735 (2018).

    PubMed 
    Article 

    Google Scholar 

  • He, S. et al. An emerging and expanding clade accounts for the persistent outbreak of coxsackievirus A6-associated hand, foot, and mouth disease in China since 2013. Virology 518, 328–334 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Anh, N. T. et al. Emerging coxsackievirus A6 causing hand, foot and mouth disease, Vietnam. Emerg. Infect. Dis. 24, 654–662 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Puenpa, J. et al. Hand, foot and mouth disease caused by coxsackievirus A6, Thailand, 2012. Emerg. Infect. Dis. 19, 641–643 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wu, Y. et al. The largest outbreak of hand; foot and mouth disease in Singapore in 2008: the role of enterovirus 71 and coxsackievirus A strains. Int. J. Infect. Dis. 14, e1076–e1081 (2010).

    PubMed 
    Article 

    Google Scholar 

  • Feder, H. M., Bennett, N. & Modlin, J. F. Atypical hand, foot, and mouth disease: a vesiculobullous eruption caused by Coxsackie virus A6. Lancet Infect. Dis. 14, 83–A86 (2014).

    PubMed 
    Article 

    Google Scholar 

  • Lott, J. P. et al. Atypical hand-foot-and-mouth disease associated with coxsackievirus A6 infection. J. Am. Acad. Dermatol. 69, 736–741 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Montes, M. et al. Hand, foot, and mouth disease outbreak and coxsackievirus A6, northern Spain, 2011. Emerg. Infect. Dis. 19, 676–678 (2013).

  • Sinclair, C. et al. Atypical hand, foot, and mouth disease associated with coxsackievirus A6 infection, Edinburgh, United Kingdom, January to February 2014. Euro Surveill. 19, 20745 (2014).

  • Drago, F., Ciccarese, G., Broccolo, F., Rebora, A. & Parodi, A. Atypical hand, foot, and mouth disease in adults. J. Am. Acad. Dermatol. 77, e51–e56 (2017).

    PubMed 
    Article 

    Google Scholar 

  • Yang, X. et al. Clinical features and phylogenetic analysis of severe hand-foot-and-mouth disease caused by Coxsackievirus A6. Infect. Genet. Evol. 77, 104054 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Blomqvist, S. et al. Co-circulation of coxsackieviruses A6 and A10 in hand, foot and mouth disease outbreak in Finland. J. Clin. Virol. 48, 49–54 (2010).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Broccolo, F. et al. Severe atypical hand-foot-and-mouth disease in adults due to coxsackievirus A6: Clinical presentation and phylogenesis of CV-A6 strains. J. Clin. Virol. 110, 1–6 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Jiang, P., Liu, Y., Ma, H.-C., Paul, A. V. & Wimmer, E. Picornavirus morphogenesis. Microbiol. Mol. Biol. Rev. 78, 418–437 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hogle, J. M. Poliovirus cell entry: common structural themes in viral cell entry pathways. Annu. Rev. Microbiol. 56, 677–702 (2002).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Harutyunyan, S. et al. Viral uncoating is directional: exit of the genomic RNA in a common cold virus starts with the poly-(A) tail at the 3′-end. PLoS Pathog. 9, e1003270 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Buchta, D. et al. Enterovirus particles expel capsid pentamers to enable genome release. Nat. Commun. 10, 1138 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Korant, B. D., Lonberg-Holm, K., Noble, J. & Stasny, J. T. Naturally occurring and artificially produced components of three rhinoviruses. Virology 48, 71–86 (1972).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Fricks, C. E. & Hogle, J. M. Cell-induced conformational change in poliovirus: externalization of the amino terminus of VP1 is responsible for liposome binding. J. Virol. 64, 1934–1945 (1990).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Plevka, P., Perera, R., Cardosa, J., Kuhn, R. J. & Rossmann, M. G. Crystal structure of human enterovirus 71. Science 336, 1274 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wang, X. et al. A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat. Struct. Mol. Biol. 19, 424 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ren, J. et al. Structures of coxsackievirus A16 capsids with native antigenicity: implications for particle expansion, receptor binding, and immunogenicity. J. Virol. 89, 10500–10511 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Xu, L. et al. Atomic structures of coxsackievirus A6 and its complex with a neutralizing antibody. Nat. Commun. 8, 505 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Chen, J. et al. A 3.0-angstrom resolution cryo-electron microscopy structure and antigenic sites of coxsackievirus A6-like particles. J. Virol. 92, e01257–01217 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lee, H. et al. The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs. Sci. Adv. 2, e1501929 (2016).

  • Belnap, D. M. et al. Molecular tectonic model of virus structural transitions: the putative cell entry states of poliovirus. J. Virol. 74, 1342–1354 (2000).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Oberste, M. S., Penaranda, S., Maher, K. & Pallansch, M. A. Complete genome sequences of all members of the species Human enterovirus A. J. Gen. Virol. 85, 1597–1607 (2004).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Chapman, M. S. & Liljas, L. in Advances in Protein Chemistry (Academic Press, 2003).

  • Krupovic, M. & Koonin, E. V. Multiple origins of viral capsid proteins from cellular ancestors. Proc. Natl Acad. Sci. USA 114, E2401–E2410 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wien, M. W., Curry, S., Filman, D. J. & Hogle, J. M. Structural studies of poliovirus mutants that overcome receptor defects. Nat. Struct. Biol. 4, 666–674 (1997).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Smyth, M., Pettitt, T., Symonds, A. & Martin, J. Identification of the pocket factors in a picornavirus. Arch. Virol. 148, 1225–1233 (2003).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Lewis, J. K., Bothner, B., Smith Thomas, J. & Siuzdak, G. Antiviral agent blocks breathing of the common cold virus. Proc. Natl Acad. Sci. USA 95, 6774–6778 (1998).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Oliveira, M. A. et al. The structure of human rhinovirus 16. Structure 1, 51–68 (1993).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Chow, M. et al. Myristylation of picornavirus capsid protein VP4 and its structural significance. Nature 327, 482–486 (1987).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Moscufo, N., Simons, J. & Chow, M. Myristoylation is important at multiple stages in poliovirus assembly. J. Virol. 65, 2372–2380 (1991).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Scouras, A. D. & Daggett, V. The dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. Protein Sci. 20, 341–352 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Zhu, R. et al. Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10. Sci. Adv. 4, eaat7459 (2018).

  • Chen, J. et al. Coxsackievirus A10 atomic structure facilitating the discovery of a broad-spectrum inhibitor against human enteroviruses. Cell Discov. 5, 4 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Foo, D. G. W. et al. Identification of neutralizing linear epitopes from the VP1 capsid protein of Enterovirus 71 using synthetic peptides. Virus Res. 125, 61–68 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Gao, F. et al. Enterovirus 71 viral capsid protein linear epitopes: identification and characterization. Virol. J. 9, 26 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Borley, D. W. et al. Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus. PLoS ONE 8, e61122 (2013).

  • Wang, L. et al. Bioinformatics-based prediction of conformational epitopes for Enterovirus A71 and Coxsackievirus A16. Sci. Rep. 11, 5701 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hadfield, A. T. et al. The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle. Structure 5, 427–441 (1997).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Chandler-Bostock, R. et al. Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. PLoS Pathog. 16, e1009146 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wilson, K. A., Holland, D. J. & Wetmore, S. D. Topology of RNA-protein nucleobase-amino acid pi-pi interactions and comparison to analogous DNA-protein pi-pi contacts. RNA 22, 696–708 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lentz, K. N. et al. Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of the three poliovirus serotypes. Structure 5, 961–978 (1997).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Jeong, E., Kim, H., Lee, S.-W. & Han, K. Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes. Mol. Cells 16, 161–167 (2003).

    CAS 
    PubMed 

    Google Scholar 

  • Schmidt, N. J., Ho, H. H. & Lennette, E. H. Propagation and isolation of group A coxsackieviruses in RD cells. J. Clin. Microbiol. 2, 183–185 (1975).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rueckert, R. R. in Comparative Virology (eds Maramorosch, K. & Kurstak, E.) (Academic Press, 1971).

  • Flint, S. J., Enquist, L. W., Racaniello, V. R. & Skalka, A. M. Principles of Virology: Molecular Biology, Pathogenesis, and Control of Animal Viruses 2nd edn (ASM Press, 2004).

  • Harland, J. & Brown, S. M. HSV growth, preparation, and assay. Methods Mol. Med. 10, 1–8 (1998).

    CAS 
    PubMed 

    Google Scholar 

  • Watson, D. H., Russell, W. C. & Wildy, P. Electron microscopic particle counts on herpes virus using the phosphotungstate negative staining technique. Virology 19, 250–260 (1963).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Carpenter, J. E., Henderson, E. P. & Grose, C. Enumeration of an extremely high particle-to-PFU ratio for Varicella-zoster virus. J. Virol. 83, 6917–6921 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Klasse, P. J. Molecular determinants of the ratio of inert to infectious virus particles. Prog. Mol. Biol. Transl. Sci. 129, 285–326 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Liu, Y. et al. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children. Science 347, 71–74 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Smith, T. J. et al. The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science 233, 1286–1293 (1986).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Curry, S., Chow, M. & Hogle, J. M. The poliovirus 135S particle is infectious. J. Virol. 70, 7125–7131 (1996).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhao, Y. et al. Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10. Nat. Commun. 11, 38 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Xu, L. et al. Cryo-EM structures reveal the molecular basis of receptor-initiated coxsackievirus uncoating. Cell Host Microbe 29, 448–462.e5 (2021).

  • Hrebik, D. et al. ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. Proc. Natl Acad. Sci. USA 118, e2024251118 (2021).

  • R Core Team. R: a language and environment for statistical computing. (Vienna, Austria, 2018).

  • Kärber, G. Beitrag zur kollektiven Behandlung pharmakologischer Reihenversuche. Naunyn-Schmiedebergs Arch. f.ür. experimentelle Pathologie und Pharmakologie 162, 480–483 (1931).

    Article 

    Google Scholar 

  • Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Vilas, J. L. et al. MonoRes: automatic and accurate estimation of local resolution for electron microscopy maps. Structure 26, 337–344.e334 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Ramírez-Aportela, E. et al. Automatic local resolution-based sharpening of cryo-EM maps. Bioinformatics 36, 765–772 (2020).

    PubMed 

    Google Scholar 

  • de la Rosa-Trevín, J. M. et al. Xmipp 3.0: an improved software suite for image processing in electron microscopy. J. Struct. Biol. 184, 321–328 (2013).

    PubMed 
    Article 

    Google Scholar 

  • de la Rosa-Trevín, J. M. et al. Scipion: a software framework toward integration, reproducibility and validation in 3D electron microscopy. J. Struct. Biol. 195, 93–99 (2016).

    PubMed 
    Article 

    Google Scholar 

  • Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. Sect. D. 67, 235–242 (2011).

    CAS 
    Article 

    Google Scholar 

  • Pettersen, E. F. et al. UCSF chimera – a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D. 66, 486–501 (2010).

    CAS 
    Article 

    Google Scholar 

  • Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. Sect. D. 75, 861–877 (2019).

    CAS 
    Article 

    Google Scholar 

  • Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. Sect. D. 67, 355–367 (2011).

    CAS 
    Article 

    Google Scholar 

  • Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. Sect. D. 66, 12–21 (2010).

    CAS 
    Article 

    Google Scholar 

  • Wiederstein, M., Gruber, M., Frank, K., Melo, F. & Sippl, M. J. Structure-based characterization of multiprotein complexes. Structure 22, 1063–1070 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wiederstein, M. & Sippl, M. J. TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D. Nucleic Acids Res. 48, W31–W35 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kabsch, W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. Sect. A 32, 922–923 (1976).

    Article 

    Google Scholar 

  • Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evolution 30, 772–780 (2013).

    CAS 
    Article 

    Google Scholar 

  • Gouet, P., Courcelle, E., Stuart, D. I. & Metoz, F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305–308 (1999).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Crameri, F. Scientific colour maps. Zenodo (2018).

  • Brewer, C. A. Colorbrewer colour maps. https://colorbrewer2.org/ (2020).

  • Pettersen, E. F. et al. UCSF chimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D. Struct. Biol. 74, 519–530 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

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