[English] 日本語
Yorodumi
- EMDB-7472: CryoEM structure of herpes simplex virus 1 capsid with associated... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7472
TitleCryoEM structure of herpes simplex virus 1 capsid with associated tegument protein complexes.
Map dataIcosahedral reconstruction of HSV-1 capsid with associated tegument proteins.
Sample
  • Virus: Human herpesvirus 1 strain KOS
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase
Function / homology
Function and homology information


chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / viral process / viral penetration into host nucleus ...chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / 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 / DNA binding
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / 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 large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / 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
Triplex capsid protein 1 / Capsid vertex component 1 / Triplex capsid protein 2 / Major capsid protein / Capsid vertex component 2 / Large tegument protein deneddylase / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHHV-1 (Herpes simplex virus type 1) / Human herpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDai XH / Zhou ZH
Funding support United States, 6 items
OrganizationGrant numberCountry
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 Director1S10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Science / Year: 2018
Title: Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes.
Authors: Xinghong Dai / Z Hong Zhou /
Abstract: Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. ...Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. Here we report cryo-electron microscopy structures of the HSV-1 capsid with CATC up to 3.5-angstrom resolution and atomic models of multiple conformers of capsid proteins VP5, VP19c, VP23, and VP26 and tegument proteins pUL17, pUL25, and pUL36. Crowning every capsid vertex are five copies of heteropentameric CATC, each containing a pUL17 monomer supporting the coiled-coil helix bundle of a pUL25 dimer and a pUL36 dimer, thus positioning their flexible domains for potential involvement in nuclear capsid egress and axonal capsid transport. Notwithstanding newly discovered fold conservation between triplex proteins and bacteriophage λ protein gpD and the previously recognized bacteriophage HK97 gp5-like fold in VP5, HSV-1 capsid proteins exhibit extraordinary diversity in forms of domain insertion and conformational polymorphism, not only for interactions with tegument proteins but also for encapsulation of large genomes.
History
DepositionFeb 20, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseMar 14, 2018-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6cgr
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7472.png

Downloads & links

-
Map

FileDownload / File: emd_7472.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of HSV-1 capsid with associated tegument proteins.
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-10.389175 - 14.209248
Average (Standard dev.)-0.00000203136 (±0.9994727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-640-640-640
Dimensions128012801280
Spacing128012801280
CellA=B=C: 1318.3999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z128012801280
origin x/y/z0.0000.0000.000
length x/y/z1318.4001318.4001318.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-640-640-640
NC/NR/NS128012801280
D min/max/mean-10.38914.209-0.000

-
Supplemental data

-
Sample components

-
Entire : Human herpesvirus 1 strain KOS

EntireName: Human herpesvirus 1 strain KOS
Components
  • Virus: Human herpesvirus 1 strain KOS
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase

-
Supramolecule #1: Human herpesvirus 1 strain KOS

SupramoleculeName: Human herpesvirus 1 strain KOS / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cultured in Vero cells. / NCBI-ID: 10306 / Sci species name: Human herpesvirus 1 strain KOS / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 1300.0 Å / T number (triangulation number): 16

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: HHV-1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 149.229047 KDa
SequenceString: MAAPNRDPPG YRYAAAMVPT GSLLSTIEVA SHRRLFDFFS RVRSDANSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPIEQPTHNY MTKIIDRRAL NAAFSLATEA IALLTGEALD GTGIGAHRQL R AIQQLARN ...String:
MAAPNRDPPG YRYAAAMVPT GSLLSTIEVA SHRRLFDFFS RVRSDANSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPIEQPTHNY MTKIIDRRAL NAAFSLATEA IALLTGEALD GTGIGAHRQL R AIQQLARN VQAVLGAFER GTADQMLHVL LEKAPPLALL LPMQRYLDNG RLATRVARAT LVAELKRSFC ETSFFLGKAG HR REAVEAW LVDLTTATQP SVAVPRLTHA DTRGRPVDGV LVTTAPIKQR LLQSFLKVED TEADVPVTYG EMVLNGANLV TAL VMGKAV RSLDDVGRHL LEMQEEQLDL NRQTLDELES APQTTRVRAD LVSIGEKLVF LEALEKRIYA ATNVPYPLVG AMDL TFVLP LGLFNPVMER FAAHAGDLVP APGHPDPRAF PPRQLFFWGK DRQVLRLSLE HAIGTVCHPS LMNVDAAVGG LNRDP VEAA NPYGAYVAAP AGPAADMQQL FLNAWGQRLA HGRVRWVAEG QMTPEQFMQP DNANLALELH PAFDFFVGVA DVELPG GDV PPAGPGEIQA TWRVVNGNLP LALCPAAFRD ARGLELGVGR HAMAPATIAA VRGAFDDRNY PAVFYLLQAA IHGSEHV FC ALARLVVQCI TSYWNNTRCA AFVNDYSLVS YVVTYLGGDL PEECMAVYRD LVAHVEALAQ LVDDFTLTGP ELGGQAQA E LNHLMRDPAL LPPLVWDCDA LMRRAALDRH RDCRVSAGGH DPVYAAACNV ATADFNRNDG QLLHNTQARA ADAADDRPH RGADWTVHHK IYYYVMVPAF SRGRCCTAGV RFDRVYATLQ NMVVPEIAPG EECPSDPVTD PAHPLHPANL VANTVNAMFH NGRVVVDGP AMLTLQVLAH NMAERTTALL CSAAPDAGAN TASTTNMRIF DGALHAGILL MAPQHLDHTI QNGDYFYPLP V HALFAGAD HVANAPNFPP ALRDLSRQVP LVPPALGANY FSSIRQPVVQ HVRESAAGEN ALTYALMAGY FKISPVALHH QL KTGLHPG FGFTVVRQDR FVTENVLFSE RASEAYFLGQ LQVARHETGG GVNFTLTQPR GNVDLGVGYT AVVATATVRN PVT DMGNLP QNFYLGRGAP PLLDNAAAVY LRNAVVAGNR LGPAQPVPVF GCAQVPRRAG MDHGQDAVCE FIATPVSTDV NYFR RPCNP RGRAAGGVYA GDKEGDVTAL MYDHGQSDPS RAFAATANPW ASQRFSYGDL LYNGAYHLNG ASPVLSPCFK FFTSA DIAA KHRCLERLIV ETGSAVSTAT AASDVQFKRP PGCRELVEDP CGLFQEAYPL TCASDPALLR SARNGEAHAR ETHFAQ YLV YDASPLKGLA L

-
Macromolecule #2: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: HHV-1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 12.108655 KDa
SequenceString:
MAVPQFHRPS TVTTDSVRAL GMRGLVLATN NSQFIMDNNH PHPQGTQGAV REFLRGQAAA LTDLGLAHAN NTFTPQPMFA GDAPAAWLR PAFGLRRTYS PFVVREPSTP GTP

-
Macromolecule #3: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: HHV-1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 50.328281 KDa
SequenceString: MKTNPLPATP SVWGGSTVEL PPTTRDTAGQ GLLRRVLRPP ISRRDGPGLP RGSGPRRAAS TLWLLGLDGT DAPPGALTPN DDTEQALDK ILRGTMRGGA ALIGSPRHHL TRQVILTDLC QPNADRAGTL LLALRHPADL PHLAHQRAPP GRQTERLGEA W GQLMEATA ...String:
MKTNPLPATP SVWGGSTVEL PPTTRDTAGQ GLLRRVLRPP ISRRDGPGLP RGSGPRRAAS TLWLLGLDGT DAPPGALTPN DDTEQALDK ILRGTMRGGA ALIGSPRHHL TRQVILTDLC QPNADRAGTL LLALRHPADL PHLAHQRAPP GRQTERLGEA W GQLMEATA LGSGRAESGC TRAGLVSFNF LVAACAASYD ARDAADAVRA HVTANYRGTR VGARLDRFSE CLRAMVHTHV FP HEVMRFF GGLVSWVTQD ELASVTAVCA GPQEAAHTGH PGRPRSAVIL PACAFVDLDA ELGLGGPGAA FLYLVFTYRQ RRD QELCCV YVIKSQLPPR GLEPALERLF GRLRITNTIH GTEDMTPPAP NRNPDFPLAG LAANPQTPRC SAGQVTNPQF ADRL YRWQP DLRGRPTART CTYAAFAELG MMPEDSPRCL HRTERFGAVS VPVVILEGVV WRPGEWRACA

-
Macromolecule #4: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: HHV-1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 34.301617 KDa
SequenceString: MLADGFETDI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LTLADVAHES FVSGGVSPDT LGLLLAYRRR FPAVITRVLP TRIVACPLD VGLTHAGTVN LRNTSPVDLC NGDPISLVPP VFEGQATDVR LDSLDLTLRF PVPLPSPLAR EIVARLVARG I RDLNPSPR ...String:
MLADGFETDI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LTLADVAHES FVSGGVSPDT LGLLLAYRRR FPAVITRVLP TRIVACPLD VGLTHAGTVN LRNTSPVDLC NGDPISLVPP VFEGQATDVR LDSLDLTLRF PVPLPSPLAR EIVARLVARG I RDLNPSPR NPGGLPDLNV LYYNGSRLSL LADVQQLGPV NAELRSLVLN MVYSITEGTT IILTLIPRLF ALSAQDGYVN AL LQMQSVT REAAQLIHPE APALMQDGER RLPLYEALVA WLTHAGQLGD TLALAPVVRV CTFDGAAVVR SGDMAPVIRY P

-
Macromolecule #5: Capsid vertex component 1

MacromoleculeName: Capsid vertex component 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HHV-1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 74.699258 KDa
SequenceString: MNAHLANEVQ YDLGHGPGRP SSLVHVIISS ECLAAAGIPL AALMRGRPGL GTAANFQVEI QTRAHATGDC TPWCTAFAAY VPADAVGEL LAPVVPAHPG LLPRASSAGG LFVSLPVVCD AQGVYDPYAV AALRLAWGSG ASCARVILFS YDELVPPNTR Y AADSTRIM ...String:
MNAHLANEVQ YDLGHGPGRP SSLVHVIISS ECLAAAGIPL AALMRGRPGL GTAANFQVEI QTRAHATGDC TPWCTAFAAY VPADAVGEL LAPVVPAHPG LLPRASSAGG LFVSLPVVCD AQGVYDPYAV AALRLAWGSG ASCARVILFS YDELVPPNTR Y AADSTRIM RVCRHLCRYV ALLGAAAPPA AKEAAAHLSM GLGESASPRP QPLARPHAGA PADPPIVGAS DPPISPEEQL TA PGGDTTA AQDVSIAQEN EEILALVQRA VQDVTRRHPV RARTGRAACG VASGLRQGAL VHQAVSGGAM GAADADAVLA GLE PPGGGR FVAPAPHGPG GEDILNDVLT LTPGTAKPRS LVEWLDRGWE ALAGGDRPDW LWSRRSISVV LRHHYGTKQR FVVV SYENS VAWGGRRARP PLLSSALATA LTEACAAERV VRPHQLSPAG QAELLLRFPA LEVPLRHPRP VLPPFDIAAE VAFTA RIHL ACLRALGQAI RAALQGGPRI SQRLRYDFGP DQRAWLGEVT RRFPILLENL MRAVEGTAPD AFFHTAYALA VLAHLG GRG GRGRRVVPLG DDLPARFADS DGHYVFDYYS TSGDTLRLNN RPIAVAMDGD VSKREQSKCR FMEAVPSTAP RRVCEQY LP GESYAYLCLG FNRRLCGIVV FPGGFAFTIN IAAYLSLSDP VARAAVLRFC RKVSSGNGRS R

-
Macromolecule #6: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HHV-1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 62.736777 KDa
SequenceString: MDPYCPFDAL DVWEHRRFIV ADSRNFITPE FPRDFWMSPV FNLPRETAAE QVVVLQAQRT AAAAALENAA MQAAELPVDI ERRLRPIER NVHEIAGALE ALETAAAAAE EADAARGDEP AGGGDGGAPP GLAVAEMEVQ IVRNDPPLRY DTNLPVDLLH M VYAGRGAT ...String:
MDPYCPFDAL DVWEHRRFIV ADSRNFITPE FPRDFWMSPV FNLPRETAAE QVVVLQAQRT AAAAALENAA MQAAELPVDI ERRLRPIER NVHEIAGALE ALETAAAAAE EADAARGDEP AGGGDGGAPP GLAVAEMEVQ IVRNDPPLRY DTNLPVDLLH M VYAGRGAT GSSGVVFGTW YRTIQDRTIT DFPLTTRSAD FRDGRMSKTF MTALVLSLQA CGRLYVGQRH YSAFECAVLC LY LLYRNTH GAADDSDRAP VTFGDLLGRL PRYLACLAAV IGTEGGRPQY RYRDDKLPKT QFAAGGGRYE HGALASHIVI ATL MHHGVL PAAPGDVPRD ASTHVNPDGV AHHDDINRAA AAFLSRGHNL FLWEDQTLLR ATANTITALG VIQRLLANGN VYAD RLNNR LQLGMLIPGA VPSEAIARGA SGSDSGAIKS GDNNLEALCA NYVLPLYRAD PAVELTQLFP GLAALCLDAQ AGRPV GSTR RVVDMSSGAR QAALVRLTAL ELINRTRTNP TPVGEVIHAH DALAIQYEQG LGLLAQQARI GLGSNTKRFS AFNVSS DYD MLYFLCLGFI PQYLSAV

-
Macromolecule #7: Large tegument protein deneddylase

MacromoleculeName: Large tegument protein deneddylase / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: HHV-1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 333.8095 KDa
SequenceString: MIAGTPPHST MERGGDRDIV VTGARNQFAP DLEPGGSVSC MRSSLSFLSL IFDVGPRDVL SAEAIEGCLV EGGEWTRATA GPGPPRMCS IVELPNFLEY PGARGGLRCV FSRVYGEVGF FGEPAAGLLE TQCPAHTFFA GPWALRPLSY TLLTIGPLGM G LFRDGDTA ...String:
MIAGTPPHST MERGGDRDIV VTGARNQFAP DLEPGGSVSC MRSSLSFLSL IFDVGPRDVL SAEAIEGCLV EGGEWTRATA GPGPPRMCS IVELPNFLEY PGARGGLRCV FSRVYGEVGF FGEPAAGLLE TQCPAHTFFA GPWALRPLSY TLLTIGPLGM G LFRDGDTA YLFDPHGLPE GTPAFIAKVR AGDMYPYLTY YTRDRPDVRW AGAMVFFVPS GPEPAAPADL TAAALHLYGA SE TYLQDEA FSERRVAITH PLRGEIAGLG EPCVGVGPRE GVGGPGPHPP TAAQSPPPTR ARRDDRASET SRGTAGPSAK PEA KRPNRA PDDVWAVALK GTPPTDPPSA DPPSADPPSA IPPPPPSAPK TPAAEAAEED DDDMRVLEMG VVPVGRHRAR YSAG LPKRR RPTWTPPSSV EDLTSGEKTK RSAPPAKTKK KSTPKGKTPV GAAVPASVPE PVLASAPPDP AGPPVAEAGE DDGPT VPAS SQALEALKTR RSPEPPGADL AQLFEAHPNV AATAVKFTAC SAALAREVAA CSRLTISALR SPYPASPGLL ELCVIF FFE RVLAFLIENG ARTHTQAGVA GPAAALLEFT LNMLPWKTAV GDFLASTRLS LADVAAHLPL VQHVLDENSL IGRLALA KL ILVARDVIRE TDAFYGELAD LELQLRAAPP ANLYTRLGEW LLERSQAHPD TLFAPATPTH PEPLLYRVQA LAKFARGE E IRVEAEDRQM REALDALARG VDAVSQHAGP LGVMPAPAGA APQGAPRPPP LGPEAVQVRL EEVRTQARRA IEGAVKEYF YRGAVYSAKA LQASDNNDRR FHVASAAVVP VVQLLESLPV FDQHTRDIAQ RAAIPAPPPI ATSPTAILLR DLIQRGQTLD APEDLAAWL SVLTDAANQG LIERKPLDEL ARSIRDINDQ QARRSSGLAE LRRFDALDAA LGQQLDSDAA FVPAPGASPY P DDGGLSPE ATRMAEEALR QARAMDAAKL TAELAPDARA RLRERARSLE AMLEGARERA KVARDAREKF LHKLQGVLRP LP DFVGLKA CPAVLATLRA SLPAGWSDLP EAVRGAPPEV TAALRADMWG LLGQYRDALE HPTPDTATAL SGLHPSFVVV LKN LFADAP ETPFLLQFFA DHAPIIAHAV SNAINAGSAA VATADPASTV DAAVRAHRVL VDAVTALGAA ASDPASPLAF LAAM ADSAA GYVKATRLAL DARVAIAQLT TLGSAAADLV VQVRRAANQP EGEHASLIQA ATRATTGARE SLAGHEGRFG GLLHA EGTA GDHSPSGRAL QELGKVIGAT RRRADELEAA TADLREKMAA QRARSSHERW AADVEAVLDR VESGAEFDVV ELRRLQ ALA GTHGYNPRDF RKRAEQALGT NAKAVTLALE TALAFNPYTP ENQRHPMLPP LAAIHRIDWS AAFGAAADTY ADMFRVD TE PLARLLRLAG GLLERAQAND GFIDYHEAVL HLSEDLGGVP ALRQYVPFFQ KGYAEYVDIR DRLDALRADA RRAIGSVA L DLAAAAEEIS AVRNDPAAAA ELVRAGVTLP CPSEDALVAC VAALERVDQS PVKDTAYADY VAFVTRQDLA DTKDAVVRA KQQRAEATER VTAGLREVLA ARERRAQLEA EGLANLKTLL KVVAVPATVA KTLDQARSAE EIADQVEILV DQTEKARELD VQAVAWLEH AQRTFETHPL SAASGDGPGL LTRQGARLQA LFDTRRRVEA LRRSLEEAEA EWDEVWGRFG RVRGGAWKSP E GFRAACEQ LRALQDTTNT VSGLRAQRDY ERLPAKYQGV LGAKSAERAG AVEELGGRVA QHADLSARLR DEVVPRVAWE MN FDTLGGL LAEFDAVAGD LAPWAVEEFR GARELIQRRM GLYSAYAKAT GQTGAGAAAA PAPLLVDLRA LDARARASAP PGQ EADPQM LRRRGEAYLR VSGGPGPLVL REATSTLDRP FAPSFLVPDG TPLQYALCFP AVTDKLGALL MCPEAACIRP PLPT DTLES ASTVTAMYVL TVINRLQLAL SDAQAANFQL FGRFVRHRQA RWGASMDAAA ELYVALVATT LTREFGCRWA QLEWG GDAA APGPPLGPQS STRHRVSFNE NDVLVALVAS SPEHIYTFWR LDLVRQHEYM HLTLPRAFQN AADSMLFVQR LTPHPD ARI RVLPAFSAGG PPTRGLMFGT RLADWRRGKL SETDPLAPWR SVPELGTERG AALGKLSPAQ ALAAVSVLGR MCLPSTA LV ALWTCMFPDD YTEYDSFDAL LTARLESGQT LSPSGGREAS PPAPPNALYR PTGQHVAVPA AATHRTPAAR VTAMDLVL A AVLLGAPVVV ALRNTTAFSR ESELELCLTL FDSRARGPDA ALRDAVSSDI ETWAVRLLHA DLNPIENACL AAQLPRLSA LIAERPLARG PPCLVLVDIS MTPVAVLWEN PDPPGPPDVR FVGSEATEEL PFVAGGEDVL AASATDEDPF LARAILGRPF DASLLSGEL FPGHPVYQRA PDDQSPSVPN PTPGPVDLVG AEGSLGPGSL APTLFTDATP GEPVPPRMWA WIHGLEELAS D DSGGPAPL LAPDPLSPTA DQSVPTSQCA PRPPGPAVTA REARPGVPAE STRPAPVGPR DDFRRLPSPQ SSPAPPDATA PR PPASSRA SAASSSGSRA RRHRRARSLA RATQASATTQ GWRPPALPDT VAPVTDFARP PAPPKPPEPA PHALVSGVPL PLG PQAAGQ ASPALPIDPV PPPVATGTVL PGGENRRPPL TSGPAPTPPR VPVGGPQRRL TRPAVASLSE SRESLPSPWD PADP TAPVL GRNPAEPTSS SPAGPSPPPP AVQPVAPPPT SGPPPTYLTL EGGVAPGGPV SRRPTTRQPV ATPTTSARPR GHLTV SRLS APQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QNGHVA PGE YPAVRFRAPQ NRPSVPASAS STNPRTGSSL SGVSSWASSL ALHIDATPPP VSLLQTLYVS DDEDSDATSL FLSDSEA EA LDPLPGEPHS PITNEPFSAL SADDSQEVTR LQFGPPPVSA NAVLSRRYVQ RTGRSALAVL IRACYRLQQQ LQRTRRAL L HHSDAVLTSL HHVRMLLG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Component - Formula: PBS / Component - Name: phosphate buffered saline
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER
Details: The sample was manually blotted and frozen with a homemade plunger..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 24271 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 14000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 79.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 2.5 µm / Digitization - Frames/image: 1-26 / Number grids imaged: 3 / Number real images: 7356 / Average exposure time: 13.0 sec. / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 45530
Details: Particles were boxed with ETHAN, and then manually examined.
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

6038

Initial angle assignmentType: COMMON LINE / Software - Name: IMIRS
Final angle assignmentType: COMMON LINE / Software - Name: IMIRS
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28042

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6cgr:
CryoEM structure of herpes simplex virus 1 capsid with associated tegument protein complexes.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more