{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T01:46:05Z","timestamp":1792028765663,"version":"4.4.0"},"reference-count":76,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2020,10,9]],"date-time":"2020-10-09T00:00:00Z","timestamp":1602201600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006280","name":"Ministerio de Ciencia y Tecnolog\u00eda","doi-asserted-by":"publisher","award":["RTI2018-095700-B-I00"],"award-info":[{"award-number":["RTI2018-095700-B-I00"]}],"id":[{"id":"10.13039\/501100006280","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006280","name":"Ministerio de Ciencia y Tecnolog\u00eda","doi-asserted-by":"publisher","award":["SEV-2016-0644"],"award-info":[{"award-number":["SEV-2016-0644"]}],"id":[{"id":"10.13039\/501100006280","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003086","name":"Eusko Jaurlaritza","doi-asserted-by":"publisher","award":["PRE_2018_1_0102"],"award-info":[{"award-number":["PRE_2018_1_0102"]}],"id":[{"id":"10.13039\/501100003086","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003086","name":"Eusko Jaurlaritza","doi-asserted-by":"publisher","award":["COVID-19 CO-2020\/00001"],"award-info":[{"award-number":["COVID-19 CO-2020\/00001"]}],"id":[{"id":"10.13039\/501100003086","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is lost. Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and thoughts that have led to the current established structure-based phylogeny of viruses: starting from the original observation that the major capsid proteins of plant and animal viruses possess similar folds, to the idea that each virus has an innate \u201cself\u201d. This latter idea fueled the conceptualization of the PRD1-adenovirus lineage whose members possess a major capsid protein (innate \u201cself\u201d) with a double jelly roll fold. Based on this approach, long-range viral evolutionary relationships can be detected allowing the virosphere to be classified in four structure-based lineages. However, this process is not without its challenges or limitations. As an example of these hurdles, we finally touch on the difficulty of establishing structural \u201cself\u201d traits for enveloped viruses showcasing the coronaviruses but also the power of structure-based analysis in the understanding of emerging viruses<\/jats:p>","DOI":"10.3390\/v12101146","type":"journal-article","created":{"date-parts":[[2020,10,13]],"date-time":"2020-10-13T22:02:02Z","timestamp":1602626522000},"page":"1146","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Superimposition of Viral Protein Structures: A Means to Decipher the Phylogenies of Viruses"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8578-7230","authenticated-orcid":false,"given":"Janne J.","family":"Ravantti","sequence":"first","affiliation":[{"name":"Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ane","family":"Martinez-Castillo","sequence":"additional","affiliation":[{"name":"Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicola G.A.","family":"Abrescia","sequence":"additional","affiliation":[{"name":"Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain"},{"name":"IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Hep\u00e1ticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,10,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1126\/science.1169202","article-title":"Extremely high mutation rate of a hammerhead viroid","volume":"323","author":"Gago","year":"2009","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Koonin, E.V., and Galperin, M.Y. (2003). Evolutionary concept in genetics and genomics. Sequence Evolution Function: Computational Approaches in Comparative Genomics, Kluwer Academic.","DOI":"10.1007\/978-1-4757-3783-7_3"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.jecp.2017.12.016","article-title":"Children\u2019s use of comparison and function in novel object categorization","volume":"170","author":"Kimura","year":"2018","journal-title":"J. Exp. Child Psychol."},{"key":"ref_4","unstructured":"Bamford, D., and Zuckerman, M. (2021). Classification of the viral world based on atomic level structures. Encyclopedia of Virology, Academic Press-Elsevier. In Press."},{"key":"ref_5","unstructured":"Bamford, D., and Zuckerman, M. (2021). Evolution steered by structure. Encyclopedia of Virology, Academic Press-Elsevier. In Press."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1126\/science.1251652","article-title":"Biochemistry. The resolution revolution","volume":"343","author":"Kuhlbrandt","year":"2014","journal-title":"Science"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/nmeth.3946","article-title":"The democratization of cryo-EM","volume":"13","author":"Stuart","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1038\/185416a0","article-title":"Structure of haemoglobin: A three-dimensional Fourier synthesis at 5.5-\u00c5. resolution, obtained by X-ray analysis","volume":"185","author":"Perutz","year":"1960","journal-title":"Nature"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/219131a0","article-title":"Three-dimensional Fourier synthesis of horse oxyhaemoglobin at 2.8 \u00c5 resolution: The atomic model","volume":"219","author":"Perutz","year":"1968","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1111\/j.1432-1033.1971.tb01285.x","article-title":"The atomic structure of erythrocruorin in the light of the chemical sequence and its comparison with myoglobin","volume":"19","author":"Huber","year":"1971","journal-title":"Eur. J. Biochem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/0022-2836(73)90388-4","article-title":"Comparison of super-secondary structures in proteins","volume":"76","author":"Rao","year":"1973","journal-title":"J. Mol. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/0022-2836(76)90195-9","article-title":"Exploring structural homology of proteins","volume":"105","author":"Rossmann","year":"1976","journal-title":"J. Mol. Biol."},{"key":"ref_13","first-page":"403","article-title":"Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming","volume":"212","author":"Sali","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2256","DOI":"10.1107\/S0907444904026460","article-title":"Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions","volume":"60","author":"Krissinel","year":"2004","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1006\/jmbi.1993.1489","article-title":"Protein structure comparison by alignment of distance matrices","volume":"233","author":"Holm","year":"1993","journal-title":"J. Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/0022-2836(79)90416-9","article-title":"Crystal structure of cat muscle pyruvate kinase at a resolution of 2.6 \u00c5","volume":"134","author":"Stuart","year":"1979","journal-title":"J. Mol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.jsb.2013.05.007","article-title":"Automatic comparison and classification of protein structures","volume":"183","author":"Ravantti","year":"2013","journal-title":"J. Struct. Biol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/276368a0","article-title":"Tomato bushy stunt virus at 2.9 \u00c5 resolution","volume":"276","author":"Harrison","year":"1978","journal-title":"Nature"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1038\/286033a0","article-title":"Structure of southern bean mosaic virus at 2.8 \u00c5 resolution","volume":"286","author":"Johnson","year":"1980","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/317145a0","article-title":"Structure of a human common cold virus and functional relationship to other picornaviruses","volume":"317","author":"Rossmann","year":"1985","journal-title":"Nature"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1126\/science.2994218","article-title":"Three-dimensional structure of poliovirus at 2.9 \u00c5 resolution","volume":"229","author":"Hogle","year":"1985","journal-title":"Science"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Burnett, R.M., Athappilly, F.K., Cai, Z., Furcinitti, P.S., Korn, A.P., Murali, R., and van Oostrum, J. (1990). Structure of the Adenovirus Virion. Use of X-ray Crystallography in the Design of Antiviral Agents, Academic Press Inc.","DOI":"10.1016\/B978-0-12-438745-4.50009-4"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature03056","article-title":"Insights into assembly from structural analysis of bacteriophage PRD1","volume":"432","author":"Abrescia","year":"2004","journal-title":"Nature"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1038\/nature03053","article-title":"Membrane structure and interactions with protein and DNA in bacteriophage PRD1","volume":"432","author":"Cockburn","year":"2004","journal-title":"Nature"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/S0065-3233(03)01004-0","article-title":"Structural folds of viral proteins","volume":"64","author":"Chapman","year":"2003","journal-title":"Adv. Protein Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1016\/S0092-8674(00)81516-0","article-title":"Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures","volume":"98","author":"Benson","year":"1999","journal-title":"Cell"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1006\/tpbi.2002.1591","article-title":"Evolution of viral structure","volume":"61","author":"Bamford","year":"2002","journal-title":"Theor. Popul. Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"14758","DOI":"10.1073\/pnas.232580699","article-title":"The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus","volume":"99","author":"Nandhagopal","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.molcel.2008.06.026","article-title":"Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2","volume":"31","author":"Abrescia","year":"2008","journal-title":"Mol. Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"7163","DOI":"10.1073\/pnas.0502164102","article-title":"Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry","volume":"102","author":"Fokine","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"10604","DOI":"10.1073\/pnas.1303047110","article-title":"Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story","volume":"110","author":"Pietila","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1016\/j.str.2011.03.023","article-title":"Insights into the evolution of a complex virus from the crystal structure of vaccinia virus d13","volume":"19","author":"Bahar","year":"2011","journal-title":"Structure"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"6206","DOI":"10.1073\/pnas.1523999113","article-title":"Structure of faustovirus, a large dsDNA virus","volume":"113","author":"Klose","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"18944","DOI":"10.1073\/pnas.0506383102","article-title":"Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses","volume":"102","author":"Khayat","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Hyun, J.K., Accurso, C., Hijnen, M., Schult, P., Pettikiriarachchi, A., Mitra, A.K., and Coulibaly, F. (2011). Membrane remodeling by the double-barrel scaffolding protein of poxvirus. PLoS Pathog., 7.","DOI":"10.1371\/journal.ppat.1002239"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.coviro.2019.02.001","article-title":"The amazingHK97 fold: Versatile results of modest differences","volume":"36","author":"Duda","year":"2019","journal-title":"Curr. Opin. Virol."},{"key":"ref_37","unstructured":"Twarock, P.G.S.R. (2010). Fry, Ravantti, Bamford, Stuart, What does it take to make a virus: The concept of the viral \u201cself\u201d. Emerging Topics in Physical Virology, Imperial College Press."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1146\/annurev-biochem-060910-095130","article-title":"Structure Unifies the Viral Universe","volume":"81","author":"Abrescia","year":"2012","journal-title":"Annu. Rev. Biochem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"D708","DOI":"10.1093\/nar\/gkx932","article-title":"Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV)","volume":"46","author":"Lefkowitz","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e02329-18","DOI":"10.1128\/mBio.02329-18","article-title":"Origins and Evolution of the Global RNA Virome","volume":"9","author":"Wolf","year":"2018","journal-title":"mBio"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1745-6150-1-29","article-title":"The ancient Virus World and evolution of cells","volume":"1","author":"Koonin","year":"2006","journal-title":"Biol. Direct."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1038\/s41579-019-0205-6","article-title":"Origin of viruses: Primordial replicators recruiting capsids from hosts","volume":"17","author":"Krupovic","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"E2401","DOI":"10.1073\/pnas.1621061114","article-title":"Multiple origins of viral capsid proteins from cellular ancestors","volume":"114","author":"Krupovic","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"International Committee on Taxonomy of Viruses Executive Committee (2020). The new scope of virus taxonomy: Partitioning the virosphere into 15 hierarchical ranks. Nat. Microbiol., 5, 668\u2013674.","DOI":"10.1038\/s41564-020-0709-x"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e00061-19","DOI":"10.1128\/MMBR.00061-19","article-title":"Global Organization and Proposed Megataxonomy of the Virus World","volume":"84","author":"Koonin","year":"2020","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"8378","DOI":"10.1073\/pnas.1703834114","article-title":"Virus found in a boreal lake links ssDNA and dsDNA viruses","volume":"114","author":"Laanto","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"18431","DOI":"10.1073\/pnas.1211702109","article-title":"Structure of Sputnik, a virophage, at 3.5-A resolution","volume":"109","author":"Zhang","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nrmicro3389","article-title":"Polintons: A hotbed of eukaryotic virus, transposon and plasmid evolution","volume":"13","author":"Krupovic","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/SQB.1962.027.001.005","article-title":"Physical principles in the construction of regular viruses","volume":"27","author":"Caspar","year":"1962","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1107\/S090744490302225X","article-title":"Structural analyses of Phycodnaviridae and Iridoviridae","volume":"59","author":"Simpson","year":"2003","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014A visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1074\/jbc.AC119.011196","article-title":"The cryo-EM structure of African swine fever virus unravels a unique architecture comprising two icosahedral protein capsids and two lipoprotein membranes","volume":"295","author":"Andres","year":"2020","journal-title":"J. Biol. Chem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1038\/s41422-019-0232-x","article-title":"Structure of the African swine fever virus major capsid protein p72","volume":"29","author":"Liu","year":"2019","journal-title":"Cell Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1016\/j.chom.2019.11.004","article-title":"Cryo-EM Structure of the African Swine Fever Virus","volume":"26","author":"Liu","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1126\/science.aaz1439","article-title":"Architecture of African swine fever virus and implications for viral assembly","volume":"366","author":"Wang","year":"2019","journal-title":"Science"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1038\/s41467-019-08319-6","article-title":"Near-atomic structure of a giant virus","volume":"10","author":"Fang","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"7332","DOI":"10.1073\/pnas.1805376115","article-title":"Capsid protein structure, self-assembly, and processing reveal morphogenesis of the marine virophage mavirus","volume":"115","author":"Born","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1006\/mthe.1999.0001","article-title":"Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon","volume":"1","author":"Rux","year":"2000","journal-title":"Mol. Ther."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/s41467-017-02707-6","article-title":"Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control","volume":"9","author":"Schmid","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/mt.2010.229","article-title":"Modifications of adenovirus hexon allow for either hepatocyte detargeting or targeting with potential evasion from Kupffer cells","volume":"19","author":"Prill","year":"2011","journal-title":"Mol. Ther."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1038\/nature25474","article-title":"A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria","volume":"554","author":"Kauffman","year":"2018","journal-title":"Nature"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.virol.2005.01.043","article-title":"SH1: A novel, spherical halovirus isolated from an Australian hypersaline lake","volume":"335","author":"Porter","year":"2005","journal-title":"Virology"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.virol.2006.07.027","article-title":"Quantitative dissociation of archaeal virus SH1 reveals distinct capsid proteins and a lipid core","volume":"356","author":"Kivela","year":"2006","journal-title":"Virology"},{"key":"ref_64","first-page":"580","article-title":"Crystallization and preliminary crystallographic analysis of the major capsid proteins VP16 and VP17 of bacteriophage P23-77","volume":"68","author":"Rissanen","year":"2012","journal-title":"Acta Crystallogr."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1866","DOI":"10.1016\/j.str.2015.07.015","article-title":"Insight into the Assembly of Viruses with Vertical Single beta-barrel Major Capsid Proteins","volume":"23","author":"Jaakkola","year":"2015","journal-title":"Structure"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1541","DOI":"10.1007\/s00705-013-1970-6","article-title":"Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae","volume":"159","author":"Pawlowski","year":"2014","journal-title":"Arch. Virol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/s41467-019-08927-2","article-title":"Structural basis for assembly of vertical single beta-barrel viruses","volume":"10","author":"Charro","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1038\/s41467-019-09451-z","article-title":"Assembly of complex viruses exemplified by a halophilic euryarchaeal virus","volume":"10","author":"Roine","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/j.virol.2015.03.043","article-title":"Viral membrane fusion","volume":"479","author":"Harrison","year":"2015","journal-title":"Virology"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.cell.2014.02.020","article-title":"Structural basis of eukaryotic cell-cell fusion","volume":"157","author":"Krey","year":"2014","journal-title":"Cell"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"8801","DOI":"10.1128\/JVI.77.16.8801-8811.2003","article-title":"The coronavirus spike protein is a class I virus fusion protein: Structural and functional characterization of the fusion core complex","volume":"77","author":"Bosch","year":"2003","journal-title":"J. Virol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"veaa003","DOI":"10.1093\/ve\/veaa003","article-title":"Unraveling virus relationships by structure-based phylogenetic classification","volume":"6","author":"Ng","year":"2020","journal-title":"Virus Evol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1002\/pro.3909","article-title":"Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein","volume":"29","author":"Ye","year":"2020","journal-title":"Protein Sci."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/s41586-020-2179-y","article-title":"Structural basis of receptor recognition by SARS-CoV-2","volume":"581","author":"Shang","year":"2020","journal-title":"Nature"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/s41586-020-2180-5","article-title":"Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor","volume":"581","author":"Lan","year":"2020","journal-title":"Nature"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.3390\/v4061011","article-title":"Mechanisms of coronavirus cell entry mediated by the viral spike protein","volume":"4","author":"Belouzard","year":"2012","journal-title":"Viruses"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/10\/1146\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:17:58Z","timestamp":1760177878000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/10\/1146"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,10,9]]},"references-count":76,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2020,10]]}},"alternative-id":["v12101146"],"URL":"https:\/\/doi.org\/10.3390\/v12101146","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,10,9]]}}}