2025-06-25 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES chem_comp_atom chem_comp_bond database_2 _database_2.pdbx_DOI _database_2.pdbx_database_accession STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name PDBj PDBj 2020-03-26 2020-09-30 2020-09-30 2025-06-25 National Natural Science Foundation of China (NSFC) 31900869 China National Natural Science Foundation of China (NSFC) 81830090 China National Natural Science Foundation of China (NSFC) 81702001 China Ministry of Science and Technology (MoST, China) 2017YFA0505600 China Ministry of Science and Technology (MoST, China) 2016YFA0502101 China Epstein-Barr virus, C1 portal-proximal penton vertex, CATC binding Li Z Yu X Zeng M Yu X portal-proximal penton vertex, CATC binding, tegumented capsid, asymmetric reconstruction, VIRAL PROTEIN Li Z Zhang X Dong L Pang J Xu M Zhong Q Zeng MS Yu X CryoEM structure of the tegumented capsid of Epstein-Barr virus. Cell Res. CN 30 873 884 2020 32620850 doi:10.1038/s41422-020-0363-0 1001-0602 7br7 FULLOVERLAP Human gammaherpesvirus 4 Human gammaherpesvirus 4 0 Human gammaherpesvirus 4 VIRION STRAIN true false Capsid vertex component 2 Epstein-Barr virus (strain B95-8) B95-8 0.062525469 2 LEVO MALSGHVLIDPARLPRDTGPELMWAPSLRNSLRVSPEALELAEREAERARSERWDRCAQVLKNRLLRVELDGIMRDHLAR AEEIRQDLDAVVAFSDGLESMQVRSPSTGGRSAPAPPSPSPAQPFTRLTGNAQYAVSISPTDPPLMVAGSLAQTLLGNLY GNINQWVPSFGPWYRTMSANAMQRRVFPKQLRGNLNFTNSVSLKLMTEVVAVLEGTTQDFFSDVRHLPDLQAALILSVAY LLLQGGSSHQQRPLPASREELLELGPESLEKIIADLKAKSPGGNFMILTSGNKEARQSIAPLNRQAAYPPGTFADNKIYN LFVGAGLLPTTAALNVPGAAGRDRDLVYRIANQIFGEDVPPFSSHQWNLRVGLAALEALMLVYTLCETANLAEAATRRLH LSSLLPQAMQRRKPAMASAGMPGAYPVQTLFRHGELFRFIWAHYVRPTVAADPQASISSLFPGLVLLALELKLMDGQAPS HYAINLTGQKFDTLFEIINQKLLFHDPAAMLAARTQLRLAFEDGVGVALGRPSPMLAAREILERQFSASDDYDRLYFLTL GYLASPVAPS P03233 Capsid vertex component 1 Epstein-Barr virus (strain B95-8) B95-8 0.054527940999999996 1 LEVO MDVHIDNQVLSGLGTPLLVHLFVPDTVMAELCPNRVPNCEGAWCQTLFSDRTGLTRVCRVFAARGMLPGRPSHRGTFTSV PVYCDEGLPELYNPFHVAALRFYDEGGLVGELQIYYLSLFEGAKRALTDGHLIREASGVQESAAAMQPIPIDPGPPGGAG IEHMPVAAAQVEHPKTYDLKQILLEITQEENRGEQRLGHAGSPALCLGLRLRAGAETKAAAETSVSKHHPALENPSNIRG SAGGEGGGGRAGTGGTVGVGSGALSRVPVSFSKTRRAIRESRALVRGIAHIFSPHALYVVTYPELSAQGRLHRMTAVTHA SPATDLAEVSILGAPEREFRFLISVALRISASFREKLAMQAWTAQQEIPVVIPTSYSRIYKNSDLIREAFFTVQTRVSWE SCWVKATISNAPKTPDACLWIDSHPLYEEGASAWGKVIDSRPPGGLVGAASQLVALGTDGHCVHLATTSDGQAFLVLPGG FVIKGQLALTPEERGYILARHGIRREQ P03222 Large tegument protein deneddylase Epstein-Barr virus (strain B95-8) B95-8 0.338310625 2 LEVO MSNGDWGQSQRTRGTGPVRGIRTMDVNAPGGGSGGSALRILGTASCNQAHCKFGRFAGIQCVSNCVLYLVKSFLAGRPLT SRPELDEVLDEGARLDALMRQSGILKGHEMAQLTDVPSSVVLRGGGRVHIYRSAEIFGLVLFPAQIANSAVVQSLAEVLH GSYNGVAQFILYICDIYAGAIIIETDGSFYLFDPHCQKDAAPGTPAHVRVSTYAHDILQYVGAPGAQYTCVHLYFLPEAF ETEDPRIFMLEHYGVYDFYEANGSGFDLVGPELVSSDGEAAGTPGADSSPPVMLPFERRIIPYNLRPLPSRSFTSDSFPA ARYSPAKTNSPPSSPASAAPASAAPASAAPASAAPASAAPASAAPASAAPASAAPASSPPLFIPIPGLGHTPGVPAPSTP PRASSGAAPQTPKRKKGLGKDSPHKKPTSGRRLPLSSTTDTEDDQLPRTHVPPHRPPSAARLPPPVIPIPHQSPPASPTP HPAPVSTIAPSVTPSPRLPLQIPIPLPQAAPSNPKIPLTTPSPSPTAAAAPTTTTLSPPPTQQQPPQSAAPAPSPLLPQQ QPTPSAAPAPSPLLPQQQPPPSAARAPSPLPPQQQPLPSATPAPPPAQQLPPSATTLEPEKNHPPAADRAGTEISPSPPF GQQPSFGDDASGGSGLVRYLSDLEEPFLSMSDSEEAESDLASDIPTTEDEDMFEDEVFSNSLESGSSAPTSPITLDTARS QYYQTTFDIETPEMDFVPLESNIARIAGHTYQEQAIVYDPASNREVPEADALSMIDYLLVTVVLEQGLIRSRDRSSVLNL LEFLKDWSGHLQVPTLDLEQLLTSELNIQNLANMLSENKGRAGEFHKHLAAKLEACLPSLATKDAVRVDAGAKMLAEIPQ LAESDDGKFDLEAARRRLTDLLSGGDQEAGEGGGEPEDNSIYRGPHVDVPLVLDDESWKRLLSLAEAARTAVARQQAGVD EEDVRFLALLTAIEYGAPPAASVPPFVHNVAVRSKNAALHVRRCTADIRDKVASAASDYLSYLEDPSLPTVMDFDDLLTH LRHTCQIIASLPLLNIRYTSIEWDYRELLYLGTALSDMSGIPWPLERVEEDDPSIAPLPEFETVAKKQKELETTRENEKR LRTILDDIEAMLGLAGVASAPGAPISPASPSATPANHDNPEATPPLADTAALTIPVIEKYIANAGSIVGAAKNPTYIRLR DTIQQIVRSKKYLMNILKSITFYTIDNYIASFEESIDHLYRDLPVLDPEVQDGIDRILDPMVSEALHTFEMGNRLTLEPA RLVALQNFATHSTLKETAAAVNLLPGLLAVYDATITGQAPEDALRLLSGLQNQLSQTLIPGKLKKRFLSYLQKLKNNNND QLRQKEVQAWRLEAEGFKPATEEQLEAFLDTAPNKELKRQYEKKLRQLMETGRKEKEKLREQEDKERQERRAREANEAWA RIRKALGARPEPAPTSPDDWNTLLASLLPDNTDSAAAAAAAVARNTDILDSLTQILAAMLLGITRVRRERLRSLLVDDGG AAERMEAAEPGWFTDIETGPLARLDAWPATPAATAKEGGGGRGAEEAAGALFRARTAADAIRSALAQTRQALQSPDMKSA VVNTDLEAPYAEYERGLAGLLEKRRAAEAALTAIVSEYVDRTLPEATNDPGQANLPPPPTIPQATAPPRLASDSALWPKK PQLLTRRERDDLLQATGDFFSELLTEAEAAEVRALEEQVRESQTLMAKAHEMAASTRRGFHTALEAVLSRSRDEAPDDEL RSLLPSPPKAPVQAPLEAALARAAAGNGSWPYRKSLAAAKWIRGICEAVRGLSEGALALAGGAGAWLNLAAAADGEIHEL TRLLEVEGMAQNSMDGMEELRLALATLDPKRVAGGKETVADWKRRLSRLEAIIQEAQEESQLQGTLQDLVTQARGHTDPR QLKIVVEAARGLALGASAGSQYALLKDKLLRYASAKQSFLAFYETAQPTVFVKHPLTNNLPLLITISAPPTGWGNGAPTR RAQFLAAAGPAKYAGTLWLETESPCDPLNPAYVSADTQEPLNYIPVYHNFLEYVMPTVLENPEAFSLTPAGRPQAIGPPQ DDQERRRRTLASVASARLSAAAADSYWDTWPDVESNAGELLREYVSAPKALMEDLADNPIVAMTLLAHASLIASRNHPPY PAPATDREVILLEQREMMALLVGTHPAYAAAFLGAPSFYAGLGLVSALARDGGLGDLLSDSVLTYRLVRSPASGRGGMPS TTRGSNDGEDARRLTRHRIAGPPTGFIFFQDAWEEMDTRAALWPHPEFLGLVHNQSTARARACMLLLARRCFAPEALQQL WHSLRPLEGPVAFQDYLRDFVKQAYTRGEELPRAEGLEVPRETPSSYGTVTGRALRNLMPYGTPITGPKRGSGDTIPVSV FEAAVAAAFLGRPLTLFVSSQYLFNLKTLGQVRVVAPLLYCDGHSEPFRSLVETISLNFLQDLDGYSESFEPEMSIFARQ AVWLRELLTEARAAKPKEARPPTVAILANRKNIIWKCFTYRHNLPDVQFYFNAAGASRWPTDVLNPSFYEHEDPPLPVGY QLPPNPRNVQELFSGFPPRVGHGLVSGDGFQSADNTPASSDRLQQLGGGETDQGEKGSTTAESEASGPPSPQSPLLEKVA PGRPRDWLSPTSSPRDVTVTPGLAAPITLPGPRLMARPYFGAETRASESPDRSPGSSPRPWPKDSLELLPQPAPQQPPSS PWASEQGPIVYTLSPHSTPSTASGSQKKHTIQIPGLVPSQKPSYPPSAPYKPGQSTGGIAPTPSAASLTTFGLQPQDTQA SSQDPPYGHSIMQREKKQQGGREEAAEIRPSATRLPTAVGLRPRAPVVAAGAAASATPAFDPGEAPSGFPIPQAPALGSG LAAPAHTPVGALAPRPQKTQAQRPQDAAALPTPTIKAVGARPVPKATGALAAGARPRGQPTAAPPSAASPPRVSLPVRSR QQQSPAIPLPPMHSGSEPGARPEVRLSQYRHAGPQTYTVRKEAPPSAASQLPKMPKCKDSMYYPPSGSARYPAPFQALSF SQSVASPAPSSDQTTLLWNTPSVVTQFLSIEDIIREVVTGGSTSGDLVVPSGSPSSLSTAAPEQDLRYSLTLSQASRVLS RFVSQLRRKLERSTHRLIADLERLKFLYL P03186 3.4.19.12 Small capsomere-interacting protein Epstein-Barr virus (strain B95-8) B95-8 0.018169099999999997 5 LEVO MARRLPKPTLQGRLEADFPDSPLLPKFQELNQNNLPNDVFREAQRSYLVFLTSQFCYEEYVQRTFGVPRRQRAIDKRQRA SVAGAGAHAHLGGSSATPVQQAQAAASAGTGALASSAPSTAVAQSATPSVSSSISSLRAATSGATAAASAAAAVDTGSGG GGQPHDTAPRGARKKQ P14348 Major capsid protein Epstein-Barr virus (strain B95-8) B95-8 0.154086828 5 LEVO MASNEGVENRPFPYLTVDADLLSNLRQSAAEGLFHSFDLLVGKDAREAGIKFEVLLGVYTNAIQYVRFLETALAVSCVNT EFKDLSRMTDGKIQFRISVPTIAHGDGRRPSKQRTFIVVKNCHKHHISTEMELSMLDLEILHSIPETPVEYAEYVGAVKT VASALQFGVDALERGLINTVLSVKLRHAPPMFILQTLADPTFTERGFSKTVKSDLIAMFKRHLLEHSFFLDRAENMGSGF SQYVRSRLSEMVAAVSGESVLKGVSTYTTAKGGEPVGGVFIVTDNVLRQLLTFLGEEADNQIMGPSSYASFVVRGENLVT AVSYGRVMRTFEHFMARIVDSPEKAGSTKSDLPAVAAGVEDQPRVPISAAVIKLGNHAVAVESLQKMYNDTQSPYPLNRR MQYSYYFPVGLFMPNPKYTTSAAIKMLDNPTQQLPVEAWIVNKNNLLLAFNLQNALKVLCHPRLHTPAHTLNSLNAAPAP RDRRETYSLQHRRPNHMNVLVIVDEFYDNKYAAPVTDIALKCGLPTEDFLHPSNYDLLRLELHPLYDIYIGRDAGERARH RAVHRLMVGNLPTPLAPAAFQEARGQQFETATSLAHVVDQAVIETVQDTAYDTAYPAFFYVVEAMIHGFEEKFVMNVPLV SLCINTYWERSGRLAFVNSFSMIKFICRHLGNNAISKEAYSMYRKIYGELIALEQALMRLAGSDVVGDESVGQYVCALLD PNLLPPVAYTDIFTHLLTVSDRAPQIIIGNEVYADTLAAPQFIERVGNMDEMAAQFVALYGYRVNGDHDHDFRLHLGPYV DEGHADVLEKIFYYVFLPTCTNAHMCGLGVDFQHVAQTLAYNGPAFSHHFTRDEDILDNLENGTLRDLLEISDLRPTVGM IRDLSASFMTCPTFTRAVRVSVDNDVTQQLAPNPADKRTEQTVLVNGLVAFAFSERTRAVTQCLFHAIPFHMFYGDPRVA ATMHQDVATFVMRNPQQRAVEAFNRPEQLFAEYREWHRSPMGKYAAECLPSLVSISGMTAMHIKMSPMAYIAQAKLKIHP GVAMTVVRTDEILSENILFSSRASTSMFIGTPNVSRREARVDAVTFEVHHEMASIDTGLSYSSTMTPARVAAITTDMGIH TQDFFSVFPAEAFGNQQVNDYIKAKVGAQRNGTLLRDPRTYLAGMTNVNGAPGLCHGQQATCEIIVTPVTADVAYFQKSN SPRGRAACVVSCENYNQEVAEGLIYDHSRPDAAYEYRSTVNPWASQLGSLGDIMYNSSYRQTAVPGLYSPCRAFFNKEEL LRNNRGLYNMVNEYSQRLGGHPATSNTEVQFVVIAGTDVFLEQPCSFLQEAFPALSASSRALIDEFMSVKQTHAPIHYGH YIIEEVAPVRRILKFGNKVVF P03226 Triplex capsid protein 1 Epstein-Barr virus (strain B95-8) B95-8 0.039231538999999996 2 LEVO MKVQGSVDRRRLQRRIAGLLPPPARRLNISRGSEFTRDVRGLVEEHAQASSLSAAAVWRAGLLAPGEVAVAGGGSGGGSF SWSGWRPPVFGDFLIHASSFNNAEATGTPLFQFKQSDPFSGVDAVFTPLSLFILMNHGRGVAARVEAGGGLTRMANLLYD SPATLADLVPDFGRLVADRRFHNFITPVGPLVENIKSTYLNKITTVVHGPVVSKAIPRSTVKVTVPQEAFVDLDAWLSGG AGGGGGVCFVGGLGLQPCPADARLYVALTYEEAGPRFTFFQSSRGHCQIMNILRIYYSPSIMHRYAVVQPLHIEELTFGA VACLGTFSATDGWRRSAFNYRGSSLPVVEIDSFYSNVSDWEVIL P03187 Triplex capsid protein 2 Epstein-Barr virus (strain B95-8) B95-8 0.033654039 4 LEVO MDLKVVVSLSSRLYTDEIAKMQQRIGCILPLASTHGTQNVQGLGLGQVYSLETVPDYVSMYNYLSDCTLAVLDEVSVDSL ILTKIVPGQTYAIKNKYQPFFQWHGTGSLSVMPPVFGREHATVKLESNDVDIVFPMVLPTPIAEEVLQKILLFNVYSRVV MQAPGNADMLDVHMHLGSVSYLGHHYELALPEVPGPLGLALLDNLSLYFCIMVTLLPRASMRLVRGLIRHEHHDLLNLFQ EMVPDEIARIDLDDLSVADDLSRMRVMMTYLQSLASLFNLGPRLATAAYSQETLTATCWLR P25214 singleParticle particle 7.5 ETHANE FEI TITAN KRIOS OTHER OTHER FIELD EMISSION GUN 300 GATAN K2 QUANTUM (4k x 4k) 48.0 1 RELION 3.0 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 4.3 FSC 0.143 CUT-OFF RELION 3.0 93334 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_30158.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 392.99997 392.99997 392.99997 90.0 90.0 90.0 X Y Z -0.040195823 0.085802935 0.0022747153 0.0067808796 1.31 1.31 1.31 0.015 AUTHOR For the entry D_1300016325, the EM map (C1) authors have provided shows a pseudo-C5 symmetry with four "ASU" copies are identity to that provided in other related entry D_1300016276. The coordinates authors uploaded only represents the unique one "ASU" due to the limitation of the chain numbers (beyond 62 chains if the model could overlap with the whole map).