ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating
Language English Country United States Media print
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
33947819
PubMed Central
PMC8126848
DOI
10.1073/pnas.2024251118
PII: 2024251118
Knihovny.cz E-resources
- Keywords
- cryo-electron microscopy, genome release, receptor, structure, virus,
- MeSH
- Virus Activation physiology MeSH
- Cryoelectron Microscopy MeSH
- Enterovirus Infections metabolism virology MeSH
- Genome, Viral genetics MeSH
- HeLa Cells MeSH
- Capsid metabolism MeSH
- Nucleic Acid Conformation MeSH
- Protein Conformation MeSH
- Crystallography, X-Ray MeSH
- Humans MeSH
- Intercellular Adhesion Molecule-1 chemistry genetics metabolism MeSH
- Models, Molecular MeSH
- Rhinovirus genetics metabolism physiology MeSH
- RNA, Viral chemistry genetics metabolism MeSH
- Amino Acid Sequence MeSH
- Sequence Homology, Amino Acid MeSH
- Virus Uncoating physiology MeSH
- Protein Binding MeSH
- Virion genetics metabolism ultrastructure MeSH
- Capsid Proteins chemistry genetics metabolism MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- ICAM1 protein, human MeSH Browser
- Intercellular Adhesion Molecule-1 MeSH
- RNA, Viral MeSH
- Capsid Proteins MeSH
Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14-ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA-VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid-RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release.
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Jacobs S. E., Lamson D. M., St George K., Walsh T. J., Human rhinoviruses. Clin. Microbiol. Rev. 26, 135–162 (2013). PubMed PMC
Fendrick A. M., Monto A. S., Nightengale B., Sarnes M., The economic burden of non-influenza-related viral respiratory tract infection in the United States. Arch. Intern. Med. 163, 487–494 (2003). PubMed
Bertino J. S., Cost burden of viral respiratory infections: Issues for formulary decision makers. Am. J. Med. 112 (suppl. 6A), 42S–49S (2002). PubMed
Palmenberg A. C., et al. ., Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science 324, 55–59 (2009). PubMed PMC
Greve J. M., et al. ., The major human rhinovirus receptor is ICAM-1. Cell 56, 839–847 (1989). PubMed
Uncapher C. R., DeWitt C. M., Colonno R. J., The major and minor group receptor families contain all but one human rhinovirus serotype. Virology 180, 814–817 (1991). PubMed
Hofer F., et al. ., Members of the low density lipoprotein receptor family mediate cell entry of a minor-group common cold virus. Proc. Natl. Acad. Sci. U.S.A. 91, 1839–1842 (1994). PubMed PMC
Bochkov Y. A., et al. ., Cadherin-related family member 3, a childhood asthma susceptibility gene product, mediates rhinovirus C binding and replication. Proc. Natl. Acad. Sci. U.S.A. 112, 5485–5490 (2015). PubMed PMC
Wells A. I., Coyne C. B., Enteroviruses: A gut-wrenching game of entry, detection, and evasion. Viruses 11, 460 (2019). PubMed PMC
Bergelson J. M., et al. ., Decay-accelerating factor (CD55), a glycosylphosphatidylinositol-anchored complement regulatory protein, is a receptor for several echoviruses. Proc. Natl. Acad. Sci. U.S.A. 91, 6245–6248 (1994). PubMed PMC
Nishimura Y., et al. ., Human P-selectin glycoprotein ligand-1 is a functional receptor for enterovirus 71. Nat. Med. 15, 794–797 (2009). PubMed
Staring J., et al. ., KREMEN1 is a host entry receptor for a major group of enteroviruses. Cell Host Microbe 23, 636–643.e5 (2018). PubMed
Su P. Y., et al. ., Cell surface sialylation affects binding of enterovirus 71 to rhabdomyosarcoma and neuroblastoma cells. BMC Microbiol. 12, 162 (2012). PubMed PMC
Mendelsohn C. L., Wimmer E., Racaniello V. R., Cellular receptor for poliovirus: Molecular cloning, nucleotide sequence, and expression of a new member of the immunoglobulin superfamily. Cell 56, 855–865 (1989). PubMed
Bergelson J. M., et al. ., Isolation of a common receptor for Coxsackie B viruses and adenoviruses 2 and 5. Science 275, 1320–1323 (1997). PubMed
Yamayoshi S., et al. ., Scavenger receptor B2 is a cellular receptor for enterovirus 71. Nat. Med. 15, 798–801 (2009). PubMed
Tuthill T. J., Groppelli E., Hogle J. M., Rowlands D. J., Picornaviruses. Curr. Top. Microbiol. Immunol. 343, 43–89 (2010). PubMed PMC
Basavappa R., et al. ., Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: Structure of the empty capsid assembly intermediate at 2.9 A resolution. Protein Sci. 3, 1651–1669 (1994). PubMed PMC
Holland J. J., Kiehn E. D., Specific cleavage of viral proteins as steps in the synthesis and maturation of enteroviruses. Proc. Natl. Acad. Sci. U.S.A. 60, 1015–1022 (1968). PubMed PMC
Procházková M., et al. ., Virion structures and genome delivery of honeybee viruses. Curr. Opin. Virol. 45, 17–24 (2020). PubMed
Rossmann M. G., et al. ., Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317, 145–153 (1985). PubMed
Harrison S. C., Olson A. J., Schutt C. E., Winkler F. K., Bricogne G., Tomato bushy stunt virus at 2.9 A resolution. Nature 276, 368–373 (1978). PubMed
Verdaguer N., Blaas D., Fita I., Structure of human rhinovirus serotype 2 (HRV2). J. Mol. Biol. 300, 1179–1194 (2000). PubMed
Oliveira M. A., et al. ., The structure of human rhinovirus 16. Structure 1, 51–68 (1993). PubMed
Smyth M., Pettitt T., Symonds A., Martin J., Identification of the pocket factors in a picornavirus. Arch. Virol. 148, 1225–1233 (2003). PubMed
Pickl-Herk A., et al. ., Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle. Proc. Natl. Acad. Sci. U.S.A. 110, 20063–20068 (2013). PubMed PMC
Levy H. C., Bostina M., Filman D. J., Hogle J. M., Catching a virus in the act of RNA release: A novel poliovirus uncoating intermediate characterized by cryo-electron microscopy. J. Virol. 84, 4426–4441 (2010). PubMed PMC
Garriga D., et al. ., Insights into minor group rhinovirus uncoating: The X-ray structure of the HRV2 empty capsid. PLoS Pathog. 8, e1002473 (2012). PubMed PMC
Wang X., et al. ., A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat. Struct. Mol. Biol. 19, 424–429 (2012). PubMed PMC
Shingler K. L., et al. ., The enterovirus 71 A-particle forms a gateway to allow genome release: A cryoEM study of picornavirus uncoating. PLoS Pathog. 9, e1003240 (2013). PubMed PMC
Seitsonen J. J., et al. ., Structural analysis of coxsackievirus A7 reveals conformational changes associated with uncoating. J. Virol. 86, 7207–7215 (2012). PubMed PMC
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). PubMed PMC
Buchta D., et al. ., Enterovirus particles expel capsid pentamers to enable genome release. Nat. Commun. 10, 1138 (2019). PubMed PMC
Ren J., et al. ., Picornavirus uncoating intermediate captured in atomic detail. Nat. Commun. 4, 1929 (2013). PubMed PMC
Bauer L., Lyoo H., van der Schaar H. M., Strating J. R., van Kuppeveld F. J., Direct-acting antivirals and host-targeting strategies to combat enterovirus infections. Curr. Opin. Virol. 24, 1–8 (2017). PubMed PMC
Smith T. J., et al. ., The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science 233, 1286–1293 (1986). PubMed
van de Stolpe A., van der Saag P. T., Intercellular adhesion molecule-1. J. Mol. Med. (Berl.) 74, 13–33 (1996). PubMed
Casasnovas J. M., Stehle T., Liu J. H., Wang J. H., Springer T. A., A dimeric crystal structure for the N-terminal two domains of intercellular adhesion molecule-1. Proc. Natl. Acad. Sci. U.S.A. 95, 4134–4139 (1998). PubMed PMC
Chothia C., Jones E. Y., The molecular structure of cell adhesion molecules. Annu. Rev. Biochem. 66, 823–862 (1997). PubMed
Wang J., Springer T. A., Structural specializations of immunoglobulin superfamily members for adhesion to integrins and viruses. Immunol. Rev. 163, 197–215 (1998). PubMed
Harpaz Y., Chothia C., Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains. J. Mol. Biol. 238, 528–539 (1994). PubMed
Kolatkar P. R., et al. ., Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor. EMBO J. 18, 6249–6259 (1999). PubMed PMC
Xiao C., et al. ., Discrimination among rhinovirus serotypes for a variant ICAM-1 receptor molecule. J. Virol. 78, 10034–10044 (2004). PubMed PMC
Xiao C., et al. ., Interaction of coxsackievirus A21 with its cellular receptor, ICAM-1. J. Virol. 75, 2444–2451 (2001). PubMed PMC
Olson N. H., et al. ., Structure of a human rhinovirus complexed with its receptor molecule. Proc. Natl. Acad. Sci. U.S.A. 90, 507–511 (1993). PubMed PMC
Xing L., Casasnovas J. M., Cheng R. H., Structural analysis of human rhinovirus complexed with ICAM-1 reveals the dynamics of receptor-mediated virus uncoating. J. Virol. 77, 6101–6107 (2003). PubMed PMC
Hoover-Litty H., Greve J. M., Formation of rhinovirus-soluble ICAM-1 complexes and conformational changes in the virion. J. Virol. 67, 390–397 (1993). PubMed PMC
Hogle J. M., Chow M., Filman D. J., Three-dimensional structure of poliovirus at 2.9 A resolution. Science 229, 1358–1365 (1985). PubMed
Muckelbauer J. K., et al. ., Structure determination of coxsackievirus B3 to 3.5 A resolution. Acta Crystallogr. D Biol. Crystallogr. 51, 871–887 (1995). PubMed
Hendry E., et al. ., The crystal structure of coxsackievirus A9: New insights into the uncoating mechanisms of enteroviruses. Structure 7, 1527–1538 (1999). PubMed
Xiao C., et al. ., The crystal structure of coxsackievirus A21 and its interaction with ICAM-1. Structure 13, 1019–1033 (2005). PubMed
McFadden E. R. Jr. et al. ., Thermal mapping of the airways in humans. J. Appl. Physiol. 58, 564–570 (1985). PubMed
Xing L., et al. ., Distinct cellular receptor interactions in poliovirus and rhinoviruses. EMBO J. 19, 1207–1216 (2000). PubMed PMC
McClelland A., et al. ., Identification of monoclonal antibody epitopes and critical residues for rhinovirus binding in domain 1 of intercellular adhesion molecule 1. Proc. Natl. Acad. Sci. U.S.A. 88, 7993–7997 (1991). PubMed PMC
Sun M. A., et al. ., Prediction of reversible disulfide based on features from local structural signatures. BMC Genomics 18, 279 (2017). PubMed PMC
Register R. B., Uncapher C. R., Naylor A. M., Lineberger D. W., Colonno R. J., Human-murine chimeras of ICAM-1 identify amino acid residues critical for rhinovirus and antibody binding. J. Virol. 65, 6589–6596 (1991). PubMed PMC
Verdaguer N., Fita I., Reithmayer M., Moser R., Blaas D., X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein. Nat. Struct. Mol. Biol. 11, 429–434 (2004). PubMed
Li Q., Yafal A. G., Lee Y. M., Hogle J., Chow M., Poliovirus neutralization by antibodies to internal epitopes of VP4 and VP1 results from reversible exposure of these sequences at physiological temperature. J. Virol. 68, 3965–3970 (1994). PubMed PMC
Lewis J. K., Bothner B., Smith T. J., Siuzdak G., Antiviral agent blocks breathing of the common cold virus. Proc. Natl. Acad. Sci. U.S.A. 95, 6774–6778 (1998). PubMed PMC
Škubník K., et al. ., Capsid opening enables genome release of iflaviruses. Sci. Adv. 7, eabd7130 (2021). PubMed PMC
Bostina M., Levy H., Filman D. J., Hogle J. M., Poliovirus RNA is released from the capsid near a twofold symmetry axis. J. Virol. 85, 776–783 (2011). PubMed PMC
Strauss M., Levy H. C., Bostina M., Filman D. J., Hogle J. M., RNA transfer from poliovirus 135S particles across membranes is mediated by long umbilical connectors. J. Virol. 87, 3903–3914 (2013). PubMed PMC
Zheng S. Q., et al. ., MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). PubMed PMC
Zhang K., Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016). PubMed PMC
Wagner T., et al. ., SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019). PubMed PMC
Scheres S. H., A Bayesian view on cryo-EM structure determination. J. Mol. Biol. 415, 406–418 (2012). PubMed PMC
Russo C. J., Henderson R., Ewald sphere correction using a single side-band image processing algorithm. Ultramicroscopy 187, 26–33 (2018). PubMed PMC
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
Vilas J. L., et al. ., MonoRes: Automatic and accurate estimation of local resolution for electron microscopy maps. Structure 26, 337–344.e4 (2018). PubMed
Ramírez-Aportela E., et al. ., Automatic local resolution-based sharpening of cryo-EM maps. Bioinformatics 36, 765–772 (2020). PubMed PMC
Kleywegt G. J., Jones T. A., xdlMAPMAN and xdlDATAMAN–Programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr. D Biol. Crystallogr. 52, 826–828 (1996). PubMed
Potterton E., Briggs P., Turkenburg M., Dodson E., A graphical user interface to the CCP4 program suite. Acta Crystallogr. D Biol. Crystallogr. 59, 1131–1137 (2003). PubMed
Pettersen E. F., et al. ., UCSF Chimera–A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). PubMed
Dong Y., et al. ., Antibody-induced uncoating of human rhinovirus B14. Proc. Natl. Acad. Sci. U.S.A. 114, 8017–8022 (2017). PubMed PMC
Murshudov G. N., et al. ., REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011). PubMed PMC
Emsley P., Cowtan K., Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). PubMed
Adams P. D., et al. ., PHENIX: A comprehensive python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). PubMed PMC
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). PubMed PMC
Chen V. B., et al. ., MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010). PubMed PMC
Barad B. A., et al. ., EMRinger: Side chain-directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015). PubMed PMC
Xiao C., Rossmann M. G., Interpretation of electron density with stereographic roadmap projections. J. Struct. Biol. 158, 182–187 (2007). PubMed PMC
Madeira F., et al. ., The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 47, W636–W641 (2019). PubMed PMC
Waterhouse A. M., Procter J. B., Martin D. M., Clamp M., Barton G. J., Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009). PubMed PMC
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