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- EMDB-21525: Structures of Capsid and Capsid-Associated Tegument Complex insid... -

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Basic information

Entry
Database: EMDB / ID: EMD-21525
TitleStructures of Capsid and Capsid-Associated Tegument Complex inside the Epstein-Barr Virus
Map dataC1 symmetric 3D reconstruction of EBV 5-fold axis sub-particles
Sample
  • Virus: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2
Keywordsgamma-herpesvirus / EBV / CATC / Structural plasticity / VIRAL PROTEIN
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / chromosome organization / viral release from host cell / viral process / viral penetration into host nucleus / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification ...T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / chromosome organization / viral release from host cell / viral process / viral penetration into host nucleus / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / DNA binding
Similarity search - Function
Gammaherpesvirus capsid / Gammaherpesvirus capsid protein / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus UL25 / Herpesvirus UL25 family ...Gammaherpesvirus capsid / Gammaherpesvirus capsid protein / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus VP23 like capsid protein / Herpesvirus capsid shell protein VP19C / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Large tegument protein deneddylase / Triplex capsid protein 1 / Capsid vertex component 1 / Major capsid protein / Capsid vertex component 2 / Small capsomere-interacting protein / Triplex capsid protein 2
Similarity search - Component
Biological speciesEpstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) / Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLiu W / Cui YX
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583, 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)1S10RR23057, 1S10OD018111, and 1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 and DMR-1548924 United States
CitationJournal: Nat Microbiol / Year: 2020
Title: Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus.
Authors: Wei Liu / Yanxiang Cui / Caiyan Wang / Zihang Li / Danyang Gong / Xinghong Dai / Guo-Qiang Bi / Ren Sun / Z Hong Zhou /
Abstract: As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been ...As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies.
History
DepositionMar 5, 2020-
Header (metadata) releaseApr 15, 2020-
Map releaseJul 15, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w2d
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6w2d
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21525.png

Downloads & links

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Map

FileDownload / File: emd_21525.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC1 symmetric 3D reconstruction of EBV 5-fold axis sub-particles
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.03454509 - 0.058136877
Average (Standard dev.)0.000761338 (±0.0053506214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0350.0580.001

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Supplemental data

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Sample components

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Entire : Human herpesvirus 4 strain B95-8

EntireName: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Components
  • Virus: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2

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Supramolecule #1: Human herpesvirus 4 strain B95-8

SupramoleculeName: Human herpesvirus 4 strain B95-8 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10377 / Sci species name: Human herpesvirus 4 strain B95-8 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 154.086828 KDa
SequenceString: MASNEGVENR PFPYLTVDAD LLSNLRQSAA EGLFHSFDLL VGKDAREAGI KFEVLLGVYT NAIQYVRFLE TALAVSCVNT EFKDLSRMT DGKIQFRISV PTIAHGDGRR PSKQRTFIVV KNCHKHHIST EMELSMLDLE ILHSIPETPV EYAEYVGAVK T VASALQFG ...String:
MASNEGVENR PFPYLTVDAD LLSNLRQSAA EGLFHSFDLL VGKDAREAGI KFEVLLGVYT NAIQYVRFLE TALAVSCVNT EFKDLSRMT DGKIQFRISV PTIAHGDGRR PSKQRTFIVV KNCHKHHIST EMELSMLDLE ILHSIPETPV EYAEYVGAVK T VASALQFG VDALERGLIN TVLSVKLRHA PPMFILQTLA DPTFTERGFS KTVKSDLIAM FKRHLLEHSF FLDRAENMGS GF SQYVRSR LSEMVAAVSG ESVLKGVSTY TTAKGGEPVG GVFIVTDNVL RQLLTFLGEE ADNQIMGPSS YASFVVRGEN LVT AVSYGR VMRTFEHFMA RIVDSPEKAG STKSDLPAVA AGVEDQPRVP ISAAVIKLGN HAVAVESLQK MYNDTQSPYP LNRR MQYSY YFPVGLFMPN PKYTTSAAIK MLDNPTQQLP VEAWIVNKNN LLLAFNLQNA LKVLCHPRLH TPAHTLNSLN AAPAP RDRR ETYSLQHRRP NHMNVLVIVD EFYDNKYAAP VTDIALKCGL PTEDFLHPSN YDLLRLELHP LYDIYIGRDA GERARH RAV HRLMVGNLPT PLAPAAFQEA RGQQFETATS LAHVVDQAVI ETVQDTAYDT AYPAFFYVVE AMIHGFEEKF VMNVPLV SL CINTYWERSG RLAFVNSFSM IKFICRHLGN NAISKEAYSM YRKIYGELIA LEQALMRLAG SDVVGDESVG QYVCALLD P NLLPPVAYTD IFTHLLTVSD RAPQIIIGNE VYADTLAAPQ FIERVGNMDE MAAQFVALYG YRVNGDHDHD FRLHLGPYV DEGHADVLEK IFYYVFLPTC TNAHMCGLGV DFQHVAQTLA YNGPAFSHHF TRDEDILDNL ENGTLRDLLE ISDLRPTVGM IRDLSASFM TCPTFTRAVR VSVDNDVTQQ LAPNPADKRT EQTVLVNGLV AFAFSERTRA VTQCLFHAIP FHMFYGDPRV A ATMHQDVA TFVMRNPQQR AVEAFNRPEQ LFAEYREWHR SPMGKYAAEC LPSLVSISGM TAMHIKMSPM AYIAQAKLKI HP GVAMTVV RTDEILSENI LFSSRASTSM FIGTPNVSRR EARVDAVTFE VHHEMASIDT GLSYSSTMTP ARVAAITTDM GIH TQDFFS VFPAEAFGNQ QVNDYIKAKV GAQRNGTLLR DPRTYLAGMT NVNGAPGLCH GQQATCEIIV TPVTADVAYF QKSN SPRGR AACVVSCENY NQEVAEGLIY DHSRPDAAYE YRSTVNPWAS QLGSLGDIMY NSSYRQTAVP GLYSPCRAFF NKEEL LRNN RGLYNMVNEY SQRLGGHPAT SNTEVQFVVI AGTDVFLEQP CSFLQEAFPA LSASSRALID EFMSVKQTHA PIHYGH YII EEVAPVRRIL KFGNKVVF

UniProtKB: Major capsid protein

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Macromolecule #2: Capsid vertex component 1

MacromoleculeName: Capsid vertex component 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 54.527941 KDa
SequenceString: MDVHIDNQVL SGLGTPLLVH LFVPDTVMAE LCPNRVPNCE GAWCQTLFSD RTGLTRVCRV FAARGMLPGR PSHRGTFTSV PVYCDEGLP ELYNPFHVAA LRFYDEGGLV GELQIYYLSL FEGAKRALTD GHLIREASGV QESAAAMQPI PIDPGPPGGA G IEHMPVAA ...String:
MDVHIDNQVL SGLGTPLLVH LFVPDTVMAE LCPNRVPNCE GAWCQTLFSD RTGLTRVCRV FAARGMLPGR PSHRGTFTSV PVYCDEGLP ELYNPFHVAA LRFYDEGGLV GELQIYYLSL FEGAKRALTD GHLIREASGV QESAAAMQPI PIDPGPPGGA G IEHMPVAA AQVEHPKTYD LKQILLEITQ EENRGEQRLG HAGSPALCLG LRLRAGAETK AAAETSVSKH HPALENPSNI RG SAGGEGG GGRAGTGGTV GVGSGALSRV PVSFSKTRRA IRESRALVRG IAHIFSPHAL YVVTYPELSA QGRLHRMTAV THA SPATDL AEVSILGAPE REFRFLISVA LRISASFREK LAMQAWTAQQ EIPVVIPTSY SRIYKNSDLI REAFFTVQTR VSWE SCWVK ATISNAPKTP DACLWIDSHP LYEEGASAWG KVIDSRPPGG LVGAASQLVA LGTDGHCVHL ATTSDGQAFL VLPGG FVIK GQLALTPEER GYILARHGIR REQ

UniProtKB: Capsid vertex component 1

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Macromolecule #3: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 62.525469 KDa
SequenceString: MALSGHVLID PARLPRDTGP ELMWAPSLRN SLRVSPEALE LAEREAERAR SERWDRCAQV LKNRLLRVEL DGIMRDHLAR AEEIRQDLD AVVAFSDGLE SMQVRSPSTG GRSAPAPPSP SPAQPFTRLT GNAQYAVSIS PTDPPLMVAG SLAQTLLGNL Y GNINQWVP ...String:
MALSGHVLID PARLPRDTGP ELMWAPSLRN SLRVSPEALE LAEREAERAR SERWDRCAQV LKNRLLRVEL DGIMRDHLAR AEEIRQDLD AVVAFSDGLE SMQVRSPSTG GRSAPAPPSP SPAQPFTRLT GNAQYAVSIS PTDPPLMVAG SLAQTLLGNL Y GNINQWVP SFGPWYRTMS ANAMQRRVFP KQLRGNLNFT NSVSLKLMTE VVAVLEGTTQ DFFSDVRHLP DLQAALILSV AY LLLQGGS SHQQRPLPAS REELLELGPE SLEKIIADLK AKSPGGNFMI LTSGNKEARQ SIAPLNRQAA YPPGTFADNK IYN LFVGAG LLPTTAALNV PGAAGRDRDL VYRIANQIFG EDVPPFSSHQ WNLRVGLAAL EALMLVYTLC ETANLAEAAT RRLH LSSLL PQAMQRRKPA MASAGMPGAY PVQTLFRHGE LFRFIWAHYV RPTVAADPQA SISSLFPGLV LLALELKLMD GQAPS HYAI NLTGQKFDTL FEIINQKLLF HDPAAMLAAR TQLRLAFEDG VGVALGRPSP MLAAREILER QFSASDDYDR LYFLTL GYL ASPVAPS

UniProtKB: Capsid vertex component 2

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Macromolecule #4: Large tegument protein deneddylase

MacromoleculeName: Large tegument protein deneddylase / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 338.310625 KDa
SequenceString: MSNGDWGQSQ RTRGTGPVRG IRTMDVNAPG GGSGGSALRI LGTASCNQAH CKFGRFAGIQ CVSNCVLYLV KSFLAGRPLT SRPELDEVL DEGARLDALM RQSGILKGHE MAQLTDVPSS VVLRGGGRVH IYRSAEIFGL VLFPAQIANS AVVQSLAEVL H GSYNGVAQ ...String:
MSNGDWGQSQ RTRGTGPVRG IRTMDVNAPG GGSGGSALRI LGTASCNQAH CKFGRFAGIQ CVSNCVLYLV KSFLAGRPLT SRPELDEVL DEGARLDALM RQSGILKGHE MAQLTDVPSS VVLRGGGRVH IYRSAEIFGL VLFPAQIANS AVVQSLAEVL H GSYNGVAQ FILYICDIYA GAIIIETDGS FYLFDPHCQK DAAPGTPAHV RVSTYAHDIL QYVGAPGAQY TCVHLYFLPE AF ETEDPRI FMLEHYGVYD FYEANGSGFD LVGPELVSSD GEAAGTPGAD SSPPVMLPFE RRIIPYNLRP LPSRSFTSDS FPA ARYSPA KTNSPPSSPA SAAPASAAPA SAAPASAAPA SAAPASAAPA SAAPASAAPA SSPPLFIPIP GLGHTPGVPA PSTP PRASS GAAPQTPKRK KGLGKDSPHK KPTSGRRLPL SSTTDTEDDQ LPRTHVPPHR PPSAARLPPP VIPIPHQSPP ASPTP HPAP VSTIAPSVTP SPRLPLQIPI PLPQAAPSNP KIPLTTPSPS PTAAAAPTTT TLSPPPTQQQ PPQSAAPAPS PLLPQQ QPT PSAAPAPSPL LPQQQPPPSA ARAPSPLPPQ QQPLPSATPA PPPAQQLPPS ATTLEPEKNH PPAADRAGTE ISPSPPF GQ QPSFGDDASG GSGLVRYLSD LEEPFLSMSD SEEAESDLAS DIPTTEDEDM FEDEVFSNSL ESGSSAPTSP ITLDTARS Q YYQTTFDIET PEMDFVPLES NIARIAGHTY QEQAIVYDPA SNREVPEADA LSMIDYLLVT VVLEQGLIRS RDRSSVLNL LEFLKDWSGH LQVPTLDLEQ LLTSELNIQN LANMLSENKG RAGEFHKHLA AKLEACLPSL ATKDAVRVDA GAKMLAEIPQ LAESDDGKF DLEAARRRLT DLLSGGDQEA GEGGGEPEDN SIYRGPHVDV PLVLDDESWK RLLSLAEAAR TAVARQQAGV D EEDVRFLA LLTAIEYGAP PAASVPPFVH NVAVRSKNAA LHVRRCTADI RDKVASAASD YLSYLEDPSL PTVMDFDDLL TH LRHTCQI IASLPLLNIR YTSIEWDYRE LLYLGTALSD MSGIPWPLER VEEDDPSIAP LPEFETVAKK QKELETTREN EKR LRTILD DIEAMLGLAG VASAPGAPIS PASPSATPAN HDNPEATPPL ADTAALTIPV IEKYIANAGS IVGAAKNPTY IRLR DTIQQ IVRSKKYLMN ILKSITFYTI DNYIASFEES IDHLYRDLPV LDPEVQDGID RILDPMVSEA LHTFEMGNRL TLEPA RLVA LQNFATHSTL KETAAAVNLL PGLLAVYDAT ITGQAPEDAL RLLSGLQNQL SQTLIPGKLK KRFLSYLQKL KNNNND QLR QKEVQAWRLE AEGFKPATEE QLEAFLDTAP NKELKRQYEK KLRQLMETGR KEKEKLREQE DKERQERRAR EANEAWA RI RKALGARPEP APTSPDDWNT LLASLLPDNT DSAAAAAAAV ARNTDILDSL TQILAAMLLG ITRVRRERLR SLLVDDGG A AERMEAAEPG WFTDIETGPL ARLDAWPATP AATAKEGGGG RGAEEAAGAL FRARTAADAI RSALAQTRQA LQSPDMKSA VVNTDLEAPY AEYERGLAGL LEKRRAAEAA LTAIVSEYVD RTLPEATNDP GQANLPPPPT IPQATAPPRL ASDSALWPKK PQLLTRRER DDLLQATGDF FSELLTEAEA AEVRALEEQV RESQTLMAKA HEMAASTRRG FHTALEAVLS RSRDEAPDDE L RSLLPSPP KAPVQAPLEA ALARAAAGNG SWPYRKSLAA AKWIRGICEA VRGLSEGALA LAGGAGAWLN LAAAADGEIH EL TRLLEVE GMAQNSMDGM EELRLALATL DPKRVAGGKE TVADWKRRLS RLEAIIQEAQ EESQLQGTLQ DLVTQARGHT DPR QLKIVV EAARGLALGA SAGSQYALLK DKLLRYASAK QSFLAFYETA QPTVFVKHPL TNNLPLLITI SAPPTGWGNG APTR RAQFL AAAGPAKYAG TLWLETESPC DPLNPAYVSA DTQEPLNYIP VYHNFLEYVM PTVLENPEAF SLTPAGRPQA IGPPQ DDQE RRRRTLASVA SARLSAAAAD SYWDTWPDVE SNAGELLREY VSAPKALMED LADNPIVAMT LLAHASLIAS RNHPPY PAP ATDREVILLE QREMMALLVG THPAYAAAFL GAPSFYAGLG LVSALARDGG LGDLLSDSVL TYRLVRSPAS GRGGMPS TT RGSNDGEDAR RLTRHRIAGP PTGFIFFQDA WEEMDTRAAL WPHPEFLGLV HNQSTARARA CMLLLARRCF APEALQQL W HSLRPLEGPV AFQDYLRDFV KQAYTRGEEL PRAEGLEVPR ETPSSYGTVT GRALRNLMPY GTPITGPKRG SGDTIPVSV FEAAVAAAFL GRPLTLFVSS QYLFNLKTLG QVRVVAPLLY CDGHSEPFRS LVETISLNFL QDLDGYSESF EPEMSIFARQ AVWLRELLT EARAAKPKEA RPPTVAILAN RKNIIWKCFT YRHNLPDVQF YFNAAGASRW PTDVLNPSFY EHEDPPLPVG Y QLPPNPRN VQELFSGFPP RVGHGLVSGD GFQSADNTPA SSDRLQQLGG GETDQGEKGS TTAESEASGP PSPQSPLLEK VA PGRPRDW LSPTSSPRDV TVTPGLAAPI TLPGPRLMAR PYFGAETRAS ESPDRSPGSS PRPWPKDSLE LLPQPAPQQP PSS PWASEQ GPIVYTLSPH STPSTASGSQ KKHTIQIPGL VPSQKPSYPP SAPYKPGQST GGIAPTPSAA SLTTFGLQPQ DTQA SSQDP PYGHSIMQRE KKQQGGREEA AEIRPSATRL PTAVGLRPRA PVVAAGAAAS ATPAFDPGEA PSGFPIPQAP ALGSG LAAP AHTPVGALAP RPQKTQAQRP QDAAALPTPT IKAVGARPVP KATGALAAGA RPRGQPTAAP PSAASPPRVS LPVRSR QQQ SPAIPLPPMH SGSEPGARPE VRLSQYRHAG PQTYTVRKEA PPSAASQLPK MPKCKDSMYY PPSGSARYPA PFQALSF SQ SVASPAPSSD QTTLLWNTPS VVTQFLSIED IIREVVTGGS TSGDLVVPSG SPSSLSTAAP EQDLRYSLTL SQASRVLS R FVSQLRRKLE RSTHRLIADL ERLKFLYL

UniProtKB: Large tegument protein deneddylase

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Macromolecule #5: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 5 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 18.1691 KDa
SequenceString:
MARRLPKPTL QGRLEADFPD SPLLPKFQEL NQNNLPNDVF REAQRSYLVF LTSQFCYEEY VQRTFGVPRR QRAIDKRQRA SVAGAGAHA HLGGSSATPV QQAQAAASAG TGALASSAPS TAVAQSATPS VSSSISSLRA ATSGATAAAS AAAAVDTGSG G GGQPHDTA PRGARKKQ

UniProtKB: Small capsomere-interacting protein

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Macromolecule #6: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 39.231539 KDa
SequenceString: MKVQGSVDRR RLQRRIAGLL PPPARRLNIS RGSEFTRDVR GLVEEHAQAS SLSAAAVWRA GLLAPGEVAV AGGGSGGGSF SWSGWRPPV FGDFLIHASS FNNAEATGTP LFQFKQSDPF SGVDAVFTPL SLFILMNHGR GVAARVEAGG GLTRMANLLY D SPATLADL ...String:
MKVQGSVDRR RLQRRIAGLL PPPARRLNIS RGSEFTRDVR GLVEEHAQAS SLSAAAVWRA GLLAPGEVAV AGGGSGGGSF SWSGWRPPV FGDFLIHASS FNNAEATGTP LFQFKQSDPF SGVDAVFTPL SLFILMNHGR GVAARVEAGG GLTRMANLLY D SPATLADL VPDFGRLVAD RRFHNFITPV GPLVENIKST YLNKITTVVH GPVVSKAIPR STVKVTVPQE AFVDLDAWLS GG AGGGGGV CFVGGLGLQP CPADARLYVA LTYEEAGPRF TFFQSSRGHC QIMNILRIYY SPSIMHRYAV VQPLHIEELT FGA VACLGT FSATDGWRRS AFNYRGSSLP VVEIDSFYSN VSDWEVIL

UniProtKB: Triplex capsid protein 1

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Macromolecule #7: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 33.654039 KDa
SequenceString: MDLKVVVSLS SRLYTDEIAK MQQRIGCILP LASTHGTQNV QGLGLGQVYS LETVPDYVSM YNYLSDCTLA VLDEVSVDSL ILTKIVPGQ TYAIKNKYQP FFQWHGTGSL SVMPPVFGRE HATVKLESND VDIVFPMVLP TPIAEEVLQK ILLFNVYSRV V MQAPGNAD ...String:
MDLKVVVSLS SRLYTDEIAK MQQRIGCILP LASTHGTQNV QGLGLGQVYS LETVPDYVSM YNYLSDCTLA VLDEVSVDSL ILTKIVPGQ TYAIKNKYQP FFQWHGTGSL SVMPPVFGRE HATVKLESND VDIVFPMVLP TPIAEEVLQK ILLFNVYSRV V MQAPGNAD MLDVHMHLGS VSYLGHHYEL ALPEVPGPLG LALLDNLSLY FCIMVTLLPR ASMRLVRGLI RHEHHDLLNL FQ EMVPDEI ARIDLDDLSV ADDLSRMRVM MTYLQSLASL FNLGPRLATA AYSQETLTAT CWLR

UniProtKB: Triplex capsid protein 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 28.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21085

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