2019-12-25 REL RCSB RCSB RCSB 2018-02-20 2018-03-14 2018-03-14 2019-12-25 National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR) DE025567 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI094386 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM071940 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1U24GM116792 United States National Institutes of Health/Office of the Director 1S10OD018111 United States National Science Foundation (NSF, United States) DBI-1338135 United States Dai XH Zhou ZH Dai X Zhou ZH Science US 360 2018 29622628 doi:10.1126/science.aao7298 1095-9203 0038 SCIEAS EMD-7472 other EM volume

The reconstruction of the full capsid with icosahedral symmetry imposed.

EMD-7473 associated EM volume

CryoEM structure of herpes simplex virus 1 capsid with associated tegument protein complexes.

Human herpesvirus 1 strain KOS Human herpesvirus 1 strain KOS 0 1 2 3 4 5 6 7

Cultured in Vero cells.

Human herpesvirus 1 strain KOS Homo sapiens 200 capsid 1300.0 16 VIRION STRAIN true false major capsid protein (MCP, VP5) Human herpesvirus 1 strain KOS KOS

MCP forms the hexons and pentons of the capsid.

LEVO MAAPNRDPPGYRYAAAMVPTGSLLSTIEVASHRRLFDFFSRVRS DANSLYDVEFDALLGSYCNTLSLVRFLELGLSVACVCTKFPELAYMNEGRVQFEVHQP LIARDGPHPIEQPTHNYMTKIIDRRALNAAFSLATEAIALLTGEALDGTGIGAHRQLR AIQQLARNVQAVLGAFERGTADQMLHVLLEKAPPLALLLPMQRYLDNGRLATRVARAT LVAELKRSFCETSFFLGKAGHRREAVEAWLVDLTTATQPSVAVPRLTHADTRGRPVDG VLVTTAPIKQRLLQSFLKVEDTEADVPVTYGEMVLNGANLVTALVMGKAVRSLDDVGR HLLEMQEEQLDLNRQTLDELESAPQTTRVRADLVSIGEKLVFLEALEKRIYAATNVPY PLVGAMDLTFVLPLGLFNPVMERFAAHAGDLVPAPGHPDPRAFPPRQLFFWGKDRQVL RLSLEHAIGTVCHPSLMNVDAAVGGLNRDPVEAANPYGAYVAAPAGPAADMQQLFLNA WGQRLAHGRVRWVAEGQMTPEQFMQPDNANLALELHPAFDFFVGVADVELPGGDVPPA GPGEIQATWRVVNGNLPLALCPAAFRDARGLELGVGRHAMAPATIAAVRGAFDDRNYP AVFYLLQAAIHGSEHVFCALARLVVQCITSYWNNTRCAAFVNDYSLVSYVVTYLGGDL PEECMAVYRDLVAHVEALAQLVDDFTLTGPELGGQAQAELNHLMRDPALLPPLVWDCD ALMRRAALDRHRDCRVSAGGHDPVYAAACNVATADFNRNDGQLLHNTQARAADAADDR PHRGADWTVHHKIYYYVMVPAFSRGRCCTAGVRFDRVYATLQNMVVPEIAPGEECPSD PVTDPAHPLHPANLVANTVNAMFHNGRVVVDGPAMLTLQVLAHNMAERTTALLCSAAP DAGANTASTTNMRIFDGALHAGILLMAPQHLDHTIQNGDYFYPLPVHALFAGADHVAN APNFPPALRDLSRQVPLVPPALGANYFSSIRQPVVQHVRESAAGENALTYALMAGYFK ISPVALHHQLKTGLHPGFGFTVVRQDRFVTENVLFSERASEAYFLGQLQVARHETGGG VNFTLTQPRGNVDLGVGYTAVVATATVRNPVTDMGNLPQNFYLGRGAPPLLDNAAAVY LRNAVVAGNRLGPAQPVPVFGCAQVPRRAGMDHGQDAVCEFIATPVSTDVNYFRRPCN PRGRAAGGVYAGDKEGDVTALMYDHGQSDPSRAFAATANPWASQRFSYGDLLYNGAYH LNGASPVLSPCFKFFTSADIAAKHRCLERLIVETGSAVSTATAASDVQFKRPPGCREL VEDPCGLFQEAYPLTCASDPALLRSARNGEAHARETHFAQYLVYDASPLKGLAL small capsid protein (SCP, VP26) Human herpesvirus 1 strain KOS KOS

SCP binds on top of the MCP in hexons.

LEVO MAVPQFHRPSTVTTDSVRALGMRGLVLATNNSQFIMDNNHPHPQ GTQGAVREFLRGQAAALTDLGLAHANNTFTPQPMFAGDAPAAWLRPAFGLRRTYSPFV VREPSTPGTP capsid triplex subunit 1 (VP19C) Human herpesvirus 1 strain KOS KOS

Complexed 1:2 with capsid triplex subunit 2 to form triplexes on the capsid shell.

LEVO MKTNPLPATPSVWGGSTVELPPTTRDTAGQGLLRRVLRPPISRR DGPGLPRGSGPRRAASTLWLLGLDGTDAPPGALTPNDDTEQALDKILRGTMRGGAALI GSPRHHLTRQVILTDLCQPNADRAGTLLLALRHPADLPHLAHQRAPPGRQTERLGEAW GQLMEATALGSGRAESGCTRAGLVSFNFLVAACAASYDARDAADAVRAHVTANYRGTR VGARLDRFSECLRAMVHTHVFPHEVMRFFGGLVSWVTQDELASVTAVCAGPQEAAHTG HPGRPRSAVILPACAFVDLDAELGLGGPGAAFLYLVFTYRQRRDQELCCVYVIKSQLP PRGLEPALERLFGRLRITNTIHGTEDMTPPAPNRNPDFPLAGLAANPQTPRCSAGQVT NPQFADRLYRWQPDLRGRPTARTCTYAAFAELGMMPEDSPRCLHRTERFGAVSVPVVI LEGVVWRPGEWRACA capsid triplex subunit 2 (VP23) Human herpesvirus 1 strain KOS KOS

Complexed 2:1 with capsid triplex subunit 1 to form triplexes on the capsid shell.

LEVO MLADGFETDIAIPSGISRPDAAALQRCEGRVVFLPTIRRQLTLA DVAHESFVSGGVSPDTLGLLLAYRRRFPAVITRVLPTRIVACPLDVGLTHAGTVNLRN TSPVDLCNGDPISLVPPVFEGQATDVRLDSLDLTLRFPVPLPSPLAREIVARLVARGI RDLNPSPRNPGGLPDLNVLYYNGSRLSLLADVQQLGPVNAELRSLVLNMVYSITEGTT IILTLIPRLFALSAQDGYVNALLQMQSVTREAAQLIHPEAPALMQDGERRLPLYEALV AWLTHAGQLGDTLALAPVVRVCTFDGAAVVRSGDMAPVIRYP tegument protein pUL17 Human herpesvirus 1 strain KOS KOS

Component of the capsid-associated tegument complex (CATC). Each CATC contains one pUL17 subunit.

LEVO MNAHLANEVQYDLGHGPGRPSSLVHVIISSECLAAAGIPLAALM RGRPGLGTAANFQVEIQTRAHATGDCTPWCTAFAAYVPADAVGELLAPVVPAHPGLLP RASSAGGLFVSLPVVCDAQGVYDPYAVAALRLAWGSGASCARVILFSYDELVPPNTRY AADSTRIMRVCRHLCRYVALLGAAAPPAAKEAAAHLSMGLGESASPRPQPLARPHAGA PADPPIVGASDPPISPEEQLTAPGGDTTAAQDVSIAQENEEILALVQRAVQDVTRRHP VRARTGRAACGVASGLRQGALVHQAVSGGAMGAADADAVLAGLEPPGGGRFVAPAPHG PGGEDILNDVLTLTPGTAKPRSLVEWLDRGWEALAGGDRPDWLWSRRSISVVLRHHYG TKQRFVVVSYENSVAWGGRRARPPLLSSALATALTEACAAERVVRPHQLSPAGQAELL LRFPALEVPLRHPRPVLPPFDIAAEVAFTARIHLACLRALGQAIRAALQGGPRISQRL RYDFGPDQRAWLGEVTRRFPILLENLMRAVEGTAPDAFFHTAYALAVLAHLGGRGGRG RRVVPLGDDLPARFADSDGHYVFDYYSTSGDTLRLNNRPIAVAMDGDVSKREQSKCRF MEAVPSTAPRRVCEQYLPGESYAYLCLGFNRRLCGIVVFPGGFAFTINIAAYLSLSDP VARAAVLRFCRKVSSGNGRSR tegument protein pUL25 Human herpesvirus 1 strain KOS KOS

Component of the capsid-associated tegument complex (CATC). Each CATC contains two pUL25 subunits.

LEVO MDPYCPFDALDVWEHRRFIVADSRNFITPEFPRDFWMSPVFNLP RETAAEQVVVLQAQRTAAAAALENAAMQAAELPVDIERRLRPIERNVHEIAGALEALE TAAAAAEEADAARGDEPAGGGDGGAPPGLAVAEMEVQIVRNDPPLRYDTNLPVDLLHM VYAGRGATGSSGVVFGTWYRTIQDRTITDFPLTTRSADFRDGRMSKTFMTALVLSLQA CGRLYVGQRHYSAFECAVLCLYLLYRNTHGAADDSDRAPVTFGDLLGRLPRYLACLAA VIGTEGGRPQYRYRDDKLPKTQFAAGGGRYEHGALASHIVIATLMHHGVLPAAPGDVP RDASTHVNPDGVAHHDDINRAAAAFLSRGHNLFLWEDQTLLRATANTITALGVIQRLL ANGNVYADRLNNRLQLGMLIPGAVPSEAIARGASGSDSGAIKSGDNNLEALCANYVLP LYRADPAVELTQLFPGLAALCLDAQAGRPVGSTRRVVDMSSGARQAALVRLTALELIN RTRTNPTPVGEVIHAHDALAIQYEQGLGLLAQQARIGLGSNTKRFSAFNVSSDYDMLY FLCLGFIPQYLSAV tegument protein pUL36 Human herpesvirus 1 strain KOS KOS

Component of the capsid-associated tegument complex (CATC). Each CATC contains two pUL36 subunits.

LEVO MIAGTPPHSTMERGGDRDIVVTGARNQFAPDLEPGGSVSCMRSS LSFLSLIFDVGPRDVLSAEAIEGCLVEGGEWTRATAGPGPPRMCSIVELPNFLEYPGA RGGLRCVFSRVYGEVGFFGEPAAGLLETQCPAHTFFAGPWALRPLSYTLLTIGPLGMG LFRDGDTAYLFDPHGLPEGTPAFIAKVRAGDMYPYLTYYTRDRPDVRWAGAMVFFVPS GPEPAAPADLTAAALHLYGASETYLQDEAFSERRVAITHPLRGEIAGLGEPCVGVGPR EGVGGPGPHPPTAAQSPPPTRARRDDRASETSRGTAGPSAKPEAKRPNRAPDDVWAVA LKGTPPTDPPSADPPSADPPSAIPPPPPSAPKTPAAEAAEEDDDDMRVLEMGVVPVGR HRARYSAGLPKRRRPTWTPPSSVEDLTSGEKTKRSAPPAKTKKKSTPKGKTPVGAAVP ASVPEPVLASAPPDPAGPPVAEAGEDDGPTVPASSQALEALKTRRSPEPPGADLAQLF EAHPNVAATAVKFTACSAALAREVAACSRLTISALRSPYPASPGLLELCVIFFFERVL AFLIENGARTHTQAGVAGPAAALLEFTLNMLPWKTAVGDFLASTRLSLADVAAHLPLV QHVLDENSLIGRLALAKLILVARDVIRETDAFYGELADLELQLRAAPPANLYTRLGEW LLERSQAHPDTLFAPATPTHPEPLLYRVQALAKFARGEEIRVEAEDRQMREALDALAR GVDAVSQHAGPLGVMPAPAGAAPQGAPRPPPLGPEAVQVRLEEVRTQARRAIEGAVKE YFYRGAVYSAKALQASDNNDRRFHVASAAVVPVVQLLESLPVFDQHTRDIAQRAAIPA PPPIATSPTAILLRDLIQRGQTLDAPEDLAAWLSVLTDAANQGLIERKPLDELARSIR DINDQQARRSSGLAELRRFDALDAALGQQLDSDAAFVPAPGASPYPDDGGLSPEATRM AEEALRQARAMDAAKLTAELAPDARARLRERARSLEAMLEGARERAKVARDAREKFLH KLQGVLRPLPDFVGLKACPAVLATLRASLPAGWSDLPEAVRGAPPEVTAALRADMWGL LGQYRDALEHPTPDTATALSGLHPSFVVVLKNLFADAPETPFLLQFFADHAPIIAHAV SNAINAGSAAVATADPASTVDAAVRAHRVLVDAVTALGAAASDPASPLAFLAAMADSA AGYVKATRLALDARVAIAQLTTLGSAAADLVVQVRRAANQPEGEHASLIQAATRATTG ARESLAGHEGRFGGLLHAEGTAGDHSPSGRALQELGKVIGATRRRADELEAATADLRE KMAAQRARSSHERWAADVEAVLDRVESGAEFDVVELRRLQALAGTHGYNPRDFRKRAE QALGTNAKAVTLALETALAFNPYTPENQRHPMLPPLAAIHRIDWSAAFGAAADTYADM FRVDTEPLARLLRLAGGLLERAQANDGFIDYHEAVLHLSEDLGGVPALRQYVPFFQKG YAEYVDIRDRLDALRADARRAIGSVALDLAAAAEEISAVRNDPAAAAELVRAGVTLPC PSEDALVACVAALERVDQSPVKDTAYADYVAFVTRQDLADTKDAVVRAKQQRAEATER VTAGLREVLAARERRAQLEAEGLANLKTLLKVVAVPATVAKTLDQARSAEEIADQVEI LVDQTEKARELDVQAVAWLEHAQRTFETHPLSAASGDGPGLLTRQGARLQALFDTRRR VEALRRSLEEAEAEWDEVWGRFGRVRGGAWKSPEGFRAACEQLRALQDTTNTVSGLRA QRDYERLPAKYQGVLGAKSAERAGAVEELGGRVAQHADLSARLRDEVVPRVAWEMNFD TLGGLLAEFDAVAGDLAPWAVEEFRGARELIQRRMGLYSAYAKATGQTGAGAAAAPAP LLVDLRALDARARASAPPGQEADPQMLRRRGEAYLRVSGGPGPLVLREATSTLDRPFA PSFLVPDGTPLQYALCFPAVTDKLGALLMCPEAACIRPPLPTDTLESASTVTAMYVLT VINRLQLALSDAQAANFQLFGRFVRHRQARWGASMDAAAELYVALVATTLTREFGCRW AQLEWGGDAAAPGPPLGPQSSTRHRVSFNENDVLVALVASSPEHIYTFWRLDLVRQHE YMHLTLPRAFQNAADSMLFVQRLTPHPDARIRVLPAFSAGGPPTRGLMFGTRLADWRR GKLSETDPLAPWRSVPELGTERGAALGKLSPAQALAAVSVLGRMCLPSTALVALWTCM FPDDYTEYDSFDALLTARLESGQTLSPSGGREASPPAPPNALYRPTGQHVAVPAAATH RTPAARVTAMDLVLAAVLLGAPVVVALRNTTAFSRESELELCLTLFDSRARGPDAALR DAVSSDIETWAVRLLHADLNPIENACLAAQLPRLSALIAERPLARGPPCLVLVDISMT PVAVLWENPDPPGPPDVRFVGSEATEELPFVAGGEDVLAASATDEDPFLARAILGRPF DASLLSGELFPGHPVYQRAPDDQSPSVPNPTPGPVDLVGAEGSLGPGSLAPTLFTDAT PGEPVPPRMWAWIHGLEELASDDSGGPAPLLAPDPLSPTADQSVPTSQCAPRPPGPAV TAREARPGVPAESTRPAPVGPRDDFRRLPSPQSSPAPPDATAPRPPASSRASAASSSG SRARRHRRARSLARATQASATTQGWRPPALPDTVAPVTDFARPPAPPKPPEPAPHALV SGVPLPLGPQAAGQASPALPIDPVPPPVATGTVLPGGENRRPPLTSGPAPTPPRVPVG GPQRRLTRPAVASLSESRESLPSPWDPADPTAPVLGRNPAEPTSSSPAGPSPPPPAVQ PVAPPPTSGPPPTYLTLEGGVAPGGPVSRRPTTRQPVATPTTSARPRGHLTVSRLSAP QPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQPQP QPQPQPQPQPQNGHVAPGEYPAVRFRAPQNRPSVPASASSTNPRTGSSLSGVSSWASS LALHIDATPPPVSLLQTLYVSDDEDSDATSLFLSDSEAEALDPLPGEPHSPITNEPFS ALSADDSQEVTRLQFGPPPVSANAVLSRRYVQRTGRSALAVLIRACYRLQQQLQRTRR ALLHHSDAVLTSLHHVRMLLG singleParticle particle 7.4 PBS phosphate buffered saline Quantifoil R2/1 COPPER 200 CARBON HOLEY ARRAY PLASMA CLEANING OTHER ETHANE 298 HOMEMADE PLUNGER

The sample was manually blotted and frozen with a homemade plunger..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 3.0 14000.0 24271.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 79.0 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 7676 7420 2.5 1-26 3 7356 13.0 25.0 1 45530

Particles were boxed with ETHAN, and then manually examined.

CTFFIND 3 EMD-6038 C5 FOURIER SPACE 3.5 FSC 0.143 CUT-OFF RELION 2.1

Subparticles of the vertex region were boxed out from the virion images using method described in Ilca et al, Nat Commun 6, 8843 (2015). These subparticles were treated as single particles and refined locally with Relion.

545340 PROJECTION MATCHING RELION 2.1 PROJECTION MATCHING RELION 2.1 RIGID BODY FIT REAL