{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T06:42:27Z","timestamp":1790836947390,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1011125","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T00:00:00Z","timestamp":1677456000000}}],"reference-count":99,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2023,2,14]],"date-time":"2023-02-14T00:00:00Z","timestamp":1676332800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Doctoral Programme in Integrative Life Science, University of Helsinki."},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2018-05851"],"award-info":[{"award-number":["2018-05851"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2018-05851"],"award-info":[{"award-number":["2018-05851"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2018-05851"],"award-info":[{"award-number":["2018-05851"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2021-05117"],"award-info":[{"award-number":["2021-05117"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["315950"],"award-info":[{"award-number":["315950"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006306","name":"Sigrid Jus\u00e9liuksen S\u00e4\u00e4ti\u00f6","doi-asserted-by":"publisher","award":["95-7202-38"],"award-info":[{"award-number":["95-7202-38"]}],"id":[{"id":"10.13039\/501100006306","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["765042"],"award-info":[{"award-number":["765042"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["799929"],"award-info":[{"award-number":["799929"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007798","name":"Helsingin Yliopiston Tiedes\u00e4\u00e4ti\u00f6","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007798","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Doctoral Programme in Integrative Life Science, University of Helsinki."},{"DOI":"10.13039\/100012623","name":"Federation of European Biochemical Societies","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012623","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Tick-borne encephalitis virus is an enveloped, pathogenic, RNA virus in the family\n                    <jats:italic>Flaviviridae<\/jats:italic>\n                    , genus\n                    <jats:italic>Flavivirus<\/jats:italic>\n                    . Viral particles are formed when the nucleocapsid, consisting of an RNA genome and multiple copies of the capsid protein, buds through the endoplasmic reticulum membrane and acquires the viral envelope and the associated proteins. The coordination of the nucleocapsid components to the sites of assembly and budding are poorly understood. Here, we investigate the interactions of the wild-type and truncated capsid proteins with membranes with biophysical methods and model membrane systems. We show that capsid protein initially binds membranes via electrostatic interactions with negatively-charged lipids, which is followed by membrane insertion. Additionally, we show that membrane-bound capsid protein can recruit viral genomic RNA. We confirm the biological relevance of the biophysical findings by using mass spectrometry to show that purified virions contain negatively-charged lipids. Our results suggest that nucleocapsid assembly is coordinated by negatively-charged membrane patches on the endoplasmic reticulum and that the capsid protein mediates direct contacts between the nucleocapsid and the membrane.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1011125","type":"journal-article","created":{"date-parts":[[2023,2,14]],"date-time":"2023-02-14T13:32:30Z","timestamp":1676381550000},"page":"e1011125","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":13,"title":["Simultaneous membrane and RNA binding by tick-borne encephalitis virus capsid protein"],"prefix":"10.1371","volume":"19","author":[{"given":"Lauri Ilmari Aurelius","family":"Pulkkinen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah Victoria","family":"Barrass","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Lindgren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hudson","family":"Pace","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna K.","family":"\u00d6verby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Anastasina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Bally","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Lundmark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7060-5871","authenticated-orcid":true,"given":"Sarah Jane","family":"Butcher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,2,14]]},"reference":[{"key":"ppat.1011125.ref001","volume-title":"Fields Virology. 6 ed","author":"BD Lindenbach","year":"2013"},{"key":"ppat.1011125.ref002","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1099\/jgv.0.000672","article-title":"ICTV virus taxonomy profile: Flaviviridae","volume":"98","author":"P Simmonds","year":"2017","journal-title":"J Gen Virol"},{"key":"ppat.1011125.ref003","doi-asserted-by":"crossref","first-page":"430","DOI":"10.12998\/wjcc.v3.i5.430","article-title":"Tick-borne encephalitis: A review of epidemiology, clinical characteristics, and management.","volume":"3","author":"P Bogovic","year":"2015","journal-title":"World J Clin Cases"},{"key":"ppat.1011125.ref004","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.antiviral.2019.01.014","article-title":"Tick-borne encephalitis in Europe and Russia: Review of pathogenesis, clinical features, therapy, and vaccines","author":"D Ruzek","year":"2019","journal-title":"Antiviral Research. Elsevier"},{"key":"ppat.1011125.ref005","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/s41467-018-02882-0","article-title":"Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody","volume":"9","author":"T F\u00fczik","year":"2018","journal-title":"Nat Commun"},{"key":"ppat.1011125.ref006","first-page":"1","article-title":"Molecular organisation of tick-borne encephalitis virus.","volume":"14","author":"LIA Pulkkinen","year":"2022","journal-title":"Viruses"},{"key":"ppat.1011125.ref007","doi-asserted-by":"crossref","first-page":"350","DOI":"10.3390\/v10070350","article-title":"Tick-borne encephalitis virus: a structural view.","volume":"10","author":"LIA Pulkkinen","year":"2018","journal-title":"Viruses"},{"key":"ppat.1011125.ref008","doi-asserted-by":"crossref","first-page":"8475","DOI":"10.1128\/jvi.71.11.8475-8481.1997","article-title":"Proteolytic activation of tick-borne encephalitis virus by furin","volume":"71","author":"K Stadler","year":"1997","journal-title":"J Virol"},{"key":"ppat.1011125.ref009","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1006\/viro.1999.0172","article-title":"Membrane fusion activity of tick-borne encephalitis virus and recombinant subviral particles in a liposomal model system","volume":"269","author":"J Corver","year":"2000","journal-title":"Virology"},{"key":"ppat.1011125.ref010","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/S1097-2765(01)00206-4","article-title":"Molecular organization of a recombinant subviral particle from tick-borne encephalitis virus","volume":"7","author":"I Ferlenghi","year":"2001","journal-title":"Mol Cell"},{"key":"ppat.1011125.ref011","doi-asserted-by":"crossref","first-page":"4370","DOI":"10.1128\/JVI.77.7.4370-4382.2003","article-title":"intracellular assembly and secretion of recombinant subviral particles from tick-borne encephalitis virus","volume":"77","author":"IC Lorenz","year":"2003","journal-title":"J Virol"},{"key":"ppat.1011125.ref012","doi-asserted-by":"crossref","first-page":"4773","DOI":"10.1128\/JVI.76.10.4773-4784.2002","article-title":"Mutations in the yellow fever virus nonstructural protein NS2A selectively block production of infectious particles","volume":"76","author":"BM K\u00fcmmerer","year":"2002","journal-title":"J Virol"},{"key":"ppat.1011125.ref013","doi-asserted-by":"crossref","first-page":"7804","DOI":"10.1128\/JVI.77.14.7804-7813.2003","article-title":"Molecular and functional analyses of Kunjin virus infectious cDNA clones demonstrate the essential roles for NS2A in virus assembly and for a nonconservative residue in NS3 in RNA replication","volume":"77","author":"WJ Liu","year":"2003","journal-title":"J Virol"},{"key":"ppat.1011125.ref014","doi-asserted-by":"crossref","first-page":"4731","DOI":"10.1128\/JVI.00002-08","article-title":"Role of nonstructural protein NS2A in flavivirus assembly","volume":"82","author":"JY Leung","year":"2008","journal-title":"J Virol"},{"key":"ppat.1011125.ref015","doi-asserted-by":"crossref","first-page":"3342","DOI":"10.1128\/JVI.02447-07","article-title":"Yellow fever virus NS3 plays an essential role in virus assembly independent of its known enzymatic functions","volume":"82","author":"CG Patkar","year":"2008","journal-title":"J Virol"},{"key":"ppat.1011125.ref016","doi-asserted-by":"crossref","first-page":"5571","DOI":"10.1128\/JVI.01933-10","article-title":"The capsid-binding nucleolar helicase DDX56 is important for infectivity of West Nile virus","volume":"85","author":"Z Xu","year":"2011","journal-title":"J Virol"},{"key":"ppat.1011125.ref017","doi-asserted-by":"crossref","first-page":"13094","DOI":"10.1128\/JVI.00704-13","article-title":"Nucleolin interacts with the dengue virus capsid protein and plays a role in formation of infectious virus particles","volume":"87","author":"CA Balinsky","year":"2013","journal-title":"J 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proteins and their role in virus assembly","volume":"90","author":"J Blazevic","year":"2016"},{"key":"ppat.1011125.ref022","first-page":"16","article-title":"Unique requirement for ESCRT factors in flavivirus particle formation on the endoplasmic reticulum","author":"K Tabata","year":"2016","journal-title":"Cell Rep"},{"key":"ppat.1011125.ref023","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.virol.2016.10.025","article-title":"The nucleolar helicase DDX56 redistributes to West Nile virus assembly sites","volume":"500","author":"CR Reid","year":"2017","journal-title":"Virology"},{"key":"ppat.1011125.ref024","first-page":"JVI.00197","article-title":"Host factor SPCS1 regulates the replication of Japanese encephalitis virus through interactions with transmembrane domains of NS2","author":"L Ma","year":"2018","journal-title":"B. 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trafficking, and pathogenicity in human intestinal Caco-2 cell monolayers","volume":"9","author":"C Yu","year":"2014","journal-title":"PLoS One"},{"key":"ppat.1011125.ref029","doi-asserted-by":"crossref","first-page":"3794","DOI":"10.1128\/jvi.68.6.3794-3802.1994","article-title":"NS2B-3 proteinase-mediated processing in the yellow fever virus structural region: in vitro and in vivo studies","volume":"68","author":"SM Amberg","year":"1994","journal-title":"J Virol"},{"key":"ppat.1011125.ref030","doi-asserted-by":"crossref","first-page":"3414","DOI":"10.1073\/pnas.0305892101","article-title":"Solution structure of dengue virus capsid protein reveals another fold","volume":"101","author":"L Ma","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1011125.ref031","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1016\/j.str.2004.04.024","article-title":"West Nile virus core protein: tetramer structure and ribbon formation","volume":"12","author":"T Dokland","year":"2004","journal-title":"Structure"},{"key":"ppat.1011125.ref032","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1016\/j.jmb.2018.02.006","article-title":"Crystal structure of the capsid protein from Zika virus","volume":"430","author":"Z Shang","year":"2018","journal-title":"J Mol Biol"},{"key":"ppat.1011125.ref033","first-page":"11","article-title":"Crystal structure of the Japanese encephalitis virus capsid protein","author":"T Poonsiri","year":"2019","journal-title":"Viruses"},{"key":"ppat.1011125.ref034","doi-asserted-by":"crossref","first-page":"102585","DOI":"10.1016\/j.jbc.2022.102585","article-title":"Tick-borne encephalitis virus capsid protein induces translational shutoff as revealed by its structural\u2013biological analysis","volume":"298","author":"M Selinger","year":"2022","journal-title":"J Biol Chem"},{"key":"ppat.1011125.ref035","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1002\/1873-3468.13857","article-title":"Characterization and in vitro assembly of tick-borne encephalitis virus C protein","volume":"594","author":"F Kaufman","year":"2020","journal-title":"FEBS Lett"},{"key":"ppat.1011125.ref036","first-page":"11","article-title":"Capsid protein structure in Zika virus reveals the flavivirus assembly process","author":"TY Tan","year":"2020","journal-title":"Nat Commun"},{"key":"ppat.1011125.ref037","article-title":"Proteome-wide cross-linking mass spectrometry to identify specific virus capsid-host interactions between tick-borne encephalitis virus and neuroblastoma cells.","author":"S V Barrass","year":"2021","journal-title":"BioRxiv:464531v2 [Preprint]"},{"key":"ppat.1011125.ref038","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1021\/acschembio.8b00231","article-title":"Partial intrinsic disorder governs the dengue capsid protein conformational ensemble","volume":"13","author":"PLS Boon","year":"2018","journal-title":"ACS Chem Biol"},{"key":"ppat.1011125.ref039","doi-asserted-by":"crossref","first-page":"13863","DOI":"10.1073\/pnas.1600544113","article-title":"Yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double-stranded RNA","volume":"113","author":"GH Samuel","year":"2016","journal-title":"Proc Natl Acad Sci"},{"key":"ppat.1011125.ref040","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1006\/viro.1997.8608","article-title":"A conserved internal hydrophobic domain mediates the stable membrane integration of the dengue virus capsid protein","volume":"233","author":"L Markoff","year":"1997","journal-title":"Virology"},{"key":"ppat.1011125.ref041","doi-asserted-by":"crossref","first-page":"3534","DOI":"10.1128\/JVI.76.7.3534-3543.2002","article-title":"Capsid protein c of tick-borne encephalitis virus tolerates large internal deletions and is a favorable target for attenuation of virulence","volume":"76","author":"RM Kofler","year":"2002","journal-title":"J Virol"},{"key":"ppat.1011125.ref042","doi-asserted-by":"crossref","first-page":"273","DOI":"10.3109\/09687688.2013.805835","article-title":"Hydrophobic segment of dengue virus C protein. Interaction with model membranes","volume":"30","author":"H Nem\u00e9sio","year":"2013","journal-title":"Mol. Membr. Biol"},{"key":"ppat.1011125.ref043","doi-asserted-by":"crossref","first-page":"8873","DOI":"10.1074\/jbc.M609919200","article-title":"The non-structural protein 4A of dengue virus is an integral membrane protein inducing membrane alterations in a 2K-regulated manner","volume":"282","author":"S Miller","year":"2007","journal-title":"J Biol Chem"},{"key":"ppat.1011125.ref044","doi-asserted-by":"crossref","first-page":"10438","DOI":"10.1128\/JVI.00986-10","article-title":"The endoplasmic reticulum provides the membrane platform for biogenesis of the flavivirus replication complex","volume":"84","author":"LK Gillespie","year":"2010","journal-title":"J Virol"},{"key":"ppat.1011125.ref045","doi-asserted-by":"crossref","first-page":"8353","DOI":"10.1128\/JVI.00696-10","article-title":"Influence of pr-M cleavage on the heterogeneity of extracellular dengue virus particles","volume":"84","author":"J Junjhon","year":"2010","journal-title":"J Virol"},{"key":"ppat.1011125.ref046","doi-asserted-by":"crossref","first-page":"e38202","DOI":"10.1371\/journal.pone.0038202","article-title":"Early dengue virus protein synthesis induces extensive rearrangement of the endoplasmic reticulum independent of the UPR and SREBP-2 pathway.","volume":"7","author":"J Pe\u00f1a","year":"2012","journal-title":"PLoS One"},{"key":"ppat.1011125.ref047","doi-asserted-by":"crossref","first-page":"12041","DOI":"10.1128\/JVI.02061-14","article-title":"The composition of West Nile Virus lipid envelope unveils a role of sphingolipid metabolism in flavivirus biogenesis","volume":"88","author":"MA Mart\u00edn-Acebes","year":"2014","journal-title":"J Virol"},{"key":"ppat.1011125.ref048","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1242\/jcs.114454","article-title":"Membrane curvature at a glance","volume":"128","author":"HT McMahon","year":"2015","journal-title":"J Cell Sci"},{"key":"ppat.1011125.ref049","doi-asserted-by":"crossref","first-page":"2113","DOI":"10.1016\/j.celrep.2017.02.014","article-title":"Ultrastructural characterization of Zika virus replication factories","volume":"18","author":"M Cortese","year":"2017","journal-title":"Cell Rep"},{"key":"ppat.1011125.ref050","first-page":"93","article-title":"Model system for the formation of tick-borne encephalitis virus replication compartments without viral RNA replication","author":"W-L Yau","year":"2019","journal-title":"J Virol"},{"key":"ppat.1011125.ref051","first-page":"5","article-title":"Dengue virus capsid protein usurps lipid droplets for viral particle formation.","author":"MM Samsa","year":"2009","journal-title":"PLoS Pathog."},{"key":"ppat.1011125.ref052","first-page":"JVI.02054","article-title":"Viperin restricts Zika virus and tick-borne encephalitis virus replication by targeting NS3 for proteasomal degradation","author":"C Panayiotou","year":"2018","journal-title":"J Virol"},{"key":"ppat.1011125.ref053","first-page":"92","article-title":"Viperin targets flavivirus virulence by inducing assembly of noninfectious capsid particles","author":"K Vonderstein","year":"2018","journal-title":"J Virol"},{"key":"ppat.1011125.ref054","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-9-40","article-title":"I-TASSER server for protein 3D structure prediction","volume":"9","author":"Y. 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