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- EMDB-7473: Subparticle refinement of HSV-1 capsid vertex region. -

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Basic information

Entry
Database: EMDB / ID: EMD-7473
TitleSubparticle refinement of HSV-1 capsid vertex region.
Map dataSubparticle refinement of HSV-1 capsid vertex region with associated tegument proteins.
Sample
  • Virus: Human herpesvirus 1 strain KOS
    • Protein or peptide: major capsid protein (MCP, VP5)
    • Protein or peptide: small capsid protein (SCP, VP26)
    • Protein or peptide: capsid triplex subunit 1 (VP19C)
    • Protein or peptide: capsid triplex subunit 2 (VP23)
    • Protein or peptide: tegument protein pUL17
    • Protein or peptide: tegument protein pUL25
    • Protein or peptide: tegument protein pUL36
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 / host cell cytoplasm / cysteine-type deubiquitinase activity / 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 speciesHuman herpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.58
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 4.58
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7473.png

Downloads & links

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Map

FileDownload / File: emd_7473.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubparticle refinement of HSV-1 capsid vertex region with associated tegument proteins.
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 4.58
Minimum - Maximum-7.806808 - 12.466985
Average (Standard dev.)-0.0000000077 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z395.520395.520395.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-7.80712.467-0.000

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Supplemental data

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Sample components

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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 (MCP, VP5)
    • Protein or peptide: small capsid protein (SCP, VP26)
    • Protein or peptide: capsid triplex subunit 1 (VP19C)
    • Protein or peptide: capsid triplex subunit 2 (VP23)
    • Protein or peptide: tegument protein pUL17
    • Protein or peptide: tegument protein pUL25
    • Protein or peptide: tegument protein pUL36

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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

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Macromolecule #1: major capsid protein (MCP, VP5)

MacromoleculeName: major capsid protein (MCP, VP5) / type: protein_or_peptide / ID: 1 / Details: MCP forms the hexons and pentons of the capsid. / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 strain KOS / Strain: KOS
SequenceString: MAAPNRDPPG YRYAAAMVPT GSLLSTIEVA SHRRLFDFFS RVRS DANSL YDVEFDALLG SYCNTLSLVR FLELGLSVAC VCTKFPELAY MNEGRVQFEV HQP LIARDG PHPIEQPTHN YMTKIIDRRA LNAAFSLATE AIALLTGEAL DGTGIGAHRQ LR AIQQLAR ...String:
MAAPNRDPPG YRYAAAMVPT GSLLSTIEVA SHRRLFDFFS RVRS DANSL YDVEFDALLG SYCNTLSLVR FLELGLSVAC VCTKFPELAY MNEGRVQFEV HQP LIARDG PHPIEQPTHN YMTKIIDRRA LNAAFSLATE AIALLTGEAL DGTGIGAHRQ LR AIQQLAR NVQAVLGAFE RGTADQMLHV LLEKAPPLAL LLPMQRYLDN GRLATRVARA T LVAELKRS FCETSFFLGK AGHRREAVEA WLVDLTTATQ PSVAVPRLTH ADTRGRPVDG VLVTTAPIK QRLLQSFLKV EDTEADVPVT YGEMVLNGAN LVTALVMGKA VRSLDDVGR HLLEMQEEQL DLNRQTLDEL ESAPQTTRVR ADLVSIGEKL VFLEALEKRI YAATNVPY P LVGAMDLTFV LPLGLFNPVM ERFAAHAGDL VPAPGHPDPR AFPPRQLFFW GKDRQVL RL SLEHAIGTVC HPSLMNVDAA VGGLNRDPVE AANPYGAYVA APAGPAADMQ QLFLNA WGQ RLAHGRVRWV AEGQMTPEQF MQPDNANLAL ELHPAFDFFV GVADVELPGG DVPPA GPGE IQATWRVVNG NLPLALCPAA FRDARGLELG VGRHAMAPAT IAAVRGAFDD RNYP AVFYL LQAAIHGSEH VFCALARLVV QCITSYWNNT RCAAFVNDYS LVSYVVTYLG GDL PEECMA VYRDLVAHVE ALAQLVDDFT LTGPELGGQA QAELNHLMRD PALLPPLVWD CD ALMRRAA LDRHRDCRVS AGGHDPVYAA ACNVATADFN RNDGQLLHNT QARAADAADD R PHRGADWT VHHKIYYYVM VPAFSRGRCC TAGVRFDRVY ATLQNMVVPE IAPGEECPSD PVTDPAHPL HPANLVANTV NAMFHNGRVV VDGPAMLTLQ VLAHNMAERT TALLCSAAP DAGANTASTT NMRIFDGALH AGILLMAPQH LDHTIQNGDY FYPLPVHALF AGADHVAN A PNFPPALRDL SRQVPLVPPA LGANYFSSIR QPVVQHVRES AAGENALTYA LMAGYFK IS PVALHHQLKT GLHPGFGFTV VRQDRFVTEN VLFSERASEA YFLGQLQVAR HETGGG VNF TLTQPRGNVD LGVGYTAVVA TATVRNPVTD MGNLPQNFYL GRGAPPLLDN AAAVY LRNA VVAGNRLGPA QPVPVFGCAQ VPRRAGMDHG QDAVCEFIAT PVSTDVNYFR RPCN PRGRA AGGVYAGDKE GDVTALMYDH GQSDPSRAFA ATANPWASQR FSYGDLLYNG AYH LNGASP VLSPCFKFFT SADIAAKHRC LERLIVETGS AVSTATAASD VQFKRPPGCR EL VEDPCGL FQEAYPLTCA SDPALLRSAR NGEAHARETH FAQYLVYDAS PLKGLAL

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Macromolecule #2: small capsid protein (SCP, VP26)

MacromoleculeName: small capsid protein (SCP, VP26) / type: protein_or_peptide / ID: 2 / Details: SCP binds on top of the MCP in hexons. / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 strain KOS / Strain: KOS
SequenceString:
MAVPQFHRPS TVTTDSVRAL GMRGLVLATN NSQFIMDNNH PHPQ GTQGA VREFLRGQAA ALTDLGLAHA NNTFTPQPMF AGDAPAAWLR PAFGLRRTYS PFV VREPST PGTP

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Macromolecule #3: capsid triplex subunit 1 (VP19C)

MacromoleculeName: capsid triplex subunit 1 (VP19C) / type: protein_or_peptide / ID: 3
Details: Complexed 1:2 with capsid triplex subunit 2 to form triplexes on the capsid shell.
Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 strain KOS / Strain: KOS
SequenceString: MKTNPLPATP SVWGGSTVEL PPTTRDTAGQ GLLRRVLRPP ISRR DGPGL PRGSGPRRAA STLWLLGLDG TDAPPGALTP NDDTEQALDK ILRGTMRGGA ALI GSPRHH LTRQVILTDL CQPNADRAGT LLLALRHPAD LPHLAHQRAP PGRQTERLGE AW GQLMEAT ...String:
MKTNPLPATP SVWGGSTVEL PPTTRDTAGQ GLLRRVLRPP ISRR DGPGL PRGSGPRRAA STLWLLGLDG TDAPPGALTP NDDTEQALDK ILRGTMRGGA ALI GSPRHH LTRQVILTDL CQPNADRAGT LLLALRHPAD LPHLAHQRAP PGRQTERLGE AW GQLMEAT ALGSGRAESG CTRAGLVSFN FLVAACAASY DARDAADAVR AHVTANYRGT R VGARLDRF SECLRAMVHT HVFPHEVMRF FGGLVSWVTQ DELASVTAVC AGPQEAAHTG HPGRPRSAV ILPACAFVDL DAELGLGGPG AAFLYLVFTY RQRRDQELCC VYVIKSQLP PRGLEPALER LFGRLRITNT IHGTEDMTPP APNRNPDFPL AGLAANPQTP RCSAGQVT N PQFADRLYRW QPDLRGRPTA RTCTYAAFAE LGMMPEDSPR CLHRTERFGA VSVPVVI LE GVVWRPGEWR ACA

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Macromolecule #4: capsid triplex subunit 2 (VP23)

MacromoleculeName: capsid triplex subunit 2 (VP23) / type: protein_or_peptide / ID: 4
Details: Complexed 2:1 with capsid triplex subunit 1 to form triplexes on the capsid shell.
Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 strain KOS / Strain: KOS
SequenceString: MLADGFETDI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LTLA DVAHE SFVSGGVSPD TLGLLLAYRR RFPAVITRVL PTRIVACPLD VGLTHAGTVN LRN TSPVDL CNGDPISLVP PVFEGQATDV RLDSLDLTLR FPVPLPSPLA REIVARLVAR GI RDLNPSP ...String:
MLADGFETDI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LTLA DVAHE SFVSGGVSPD TLGLLLAYRR RFPAVITRVL PTRIVACPLD VGLTHAGTVN LRN TSPVDL CNGDPISLVP PVFEGQATDV RLDSLDLTLR FPVPLPSPLA REIVARLVAR GI RDLNPSP RNPGGLPDLN VLYYNGSRLS LLADVQQLGP VNAELRSLVL NMVYSITEGT T IILTLIPR LFALSAQDGY VNALLQMQSV TREAAQLIHP EAPALMQDGE RRLPLYEALV AWLTHAGQL GDTLALAPVV RVCTFDGAAV VRSGDMAPVI RYP

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Macromolecule #5: tegument protein pUL17

MacromoleculeName: tegument protein pUL17 / type: protein_or_peptide / ID: 5
Details: Component of the capsid-associated tegument complex (CATC). Each CATC contains one pUL17 subunit.
Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 strain KOS / Strain: KOS
SequenceString: MNAHLANEVQ YDLGHGPGRP SSLVHVIISS ECLAAAGIPL AALM RGRPG LGTAANFQVE IQTRAHATGD CTPWCTAFAA YVPADAVGEL LAPVVPAHPG LLP RASSAG GLFVSLPVVC DAQGVYDPYA VAALRLAWGS GASCARVILF SYDELVPPNT RY AADSTRI ...String:
MNAHLANEVQ YDLGHGPGRP SSLVHVIISS ECLAAAGIPL AALM RGRPG LGTAANFQVE IQTRAHATGD CTPWCTAFAA YVPADAVGEL LAPVVPAHPG LLP RASSAG GLFVSLPVVC DAQGVYDPYA VAALRLAWGS GASCARVILF SYDELVPPNT RY AADSTRI MRVCRHLCRY VALLGAAAPP AAKEAAAHLS MGLGESASPR PQPLARPHAG A PADPPIVG ASDPPISPEE QLTAPGGDTT AAQDVSIAQE NEEILALVQR AVQDVTRRHP VRARTGRAA CGVASGLRQG ALVHQAVSGG AMGAADADAV LAGLEPPGGG RFVAPAPHG PGGEDILNDV LTLTPGTAKP RSLVEWLDRG WEALAGGDRP DWLWSRRSIS VVLRHHYG T KQRFVVVSYE NSVAWGGRRA RPPLLSSALA TALTEACAAE RVVRPHQLSP AGQAELL LR FPALEVPLRH PRPVLPPFDI AAEVAFTARI HLACLRALGQ AIRAALQGGP RISQRL RYD FGPDQRAWLG EVTRRFPILL ENLMRAVEGT APDAFFHTAY ALAVLAHLGG RGGRG RRVV PLGDDLPARF ADSDGHYVFD YYSTSGDTLR LNNRPIAVAM DGDVSKREQS KCRF MEAVP STAPRRVCEQ YLPGESYAYL CLGFNRRLCG IVVFPGGFAF TINIAAYLSL SDP VARAAV LRFCRKVSSG NGRSR

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Macromolecule #6: tegument protein pUL25

MacromoleculeName: tegument protein pUL25 / type: protein_or_peptide / ID: 6
Details: Component of the capsid-associated tegument complex (CATC). Each CATC contains two pUL25 subunits.
Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 strain KOS / Strain: KOS
SequenceString: MDPYCPFDAL DVWEHRRFIV ADSRNFITPE FPRDFWMSPV FNLP RETAA EQVVVLQAQR TAAAAALENA AMQAAELPVD IERRLRPIER NVHEIAGALE ALE TAAAAA EEADAARGDE PAGGGDGGAP PGLAVAEMEV QIVRNDPPLR YDTNLPVDLL HM VYAGRGA ...String:
MDPYCPFDAL DVWEHRRFIV ADSRNFITPE FPRDFWMSPV FNLP RETAA EQVVVLQAQR TAAAAALENA AMQAAELPVD IERRLRPIER NVHEIAGALE ALE TAAAAA EEADAARGDE PAGGGDGGAP PGLAVAEMEV QIVRNDPPLR YDTNLPVDLL HM VYAGRGA TGSSGVVFGT WYRTIQDRTI TDFPLTTRSA DFRDGRMSKT FMTALVLSLQ A CGRLYVGQ RHYSAFECAV LCLYLLYRNT HGAADDSDRA PVTFGDLLGR LPRYLACLAA VIGTEGGRP QYRYRDDKLP KTQFAAGGGR YEHGALASHI VIATLMHHGV LPAAPGDVP RDASTHVNPD GVAHHDDINR AAAAFLSRGH NLFLWEDQTL LRATANTITA LGVIQRLL A NGNVYADRLN NRLQLGMLIP GAVPSEAIAR GASGSDSGAI KSGDNNLEAL CANYVLP LY RADPAVELTQ LFPGLAALCL DAQAGRPVGS TRRVVDMSSG ARQAALVRLT ALELIN RTR TNPTPVGEVI HAHDALAIQY EQGLGLLAQQ ARIGLGSNTK RFSAFNVSSD YDMLY FLCL GFIPQYLSAV

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Macromolecule #7: tegument protein pUL36

MacromoleculeName: tegument protein pUL36 / type: protein_or_peptide / ID: 7
Details: Component of the capsid-associated tegument complex (CATC). Each CATC contains two pUL36 subunits.
Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 strain KOS / Strain: KOS
SequenceString: MIAGTPPHST MERGGDRDIV VTGARNQFAP DLEPGGSVSC MRSS LSFLS LIFDVGPRDV LSAEAIEGCL VEGGEWTRAT AGPGPPRMCS IVELPNFLEY PGA RGGLRC VFSRVYGEVG FFGEPAAGLL ETQCPAHTFF AGPWALRPLS YTLLTIGPLG MG LFRDGDT ...String:
MIAGTPPHST MERGGDRDIV VTGARNQFAP DLEPGGSVSC MRSS LSFLS LIFDVGPRDV LSAEAIEGCL VEGGEWTRAT AGPGPPRMCS IVELPNFLEY PGA RGGLRC VFSRVYGEVG FFGEPAAGLL ETQCPAHTFF AGPWALRPLS YTLLTIGPLG MG LFRDGDT AYLFDPHGLP EGTPAFIAKV RAGDMYPYLT YYTRDRPDVR WAGAMVFFVP S GPEPAAPA DLTAAALHLY GASETYLQDE AFSERRVAIT HPLRGEIAGL GEPCVGVGPR EGVGGPGPH PPTAAQSPPP TRARRDDRAS ETSRGTAGPS AKPEAKRPNR APDDVWAVA LKGTPPTDPP SADPPSADPP SAIPPPPPSA PKTPAAEAAE EDDDDMRVLE MGVVPVGR H RARYSAGLPK RRRPTWTPPS SVEDLTSGEK TKRSAPPAKT KKKSTPKGKT PVGAAVP AS VPEPVLASAP PDPAGPPVAE AGEDDGPTVP ASSQALEALK TRRSPEPPGA DLAQLF EAH PNVAATAVKF TACSAALARE VAACSRLTIS ALRSPYPASP GLLELCVIFF FERVL AFLI ENGARTHTQA GVAGPAAALL EFTLNMLPWK TAVGDFLAST RLSLADVAAH LPLV QHVLD ENSLIGRLAL AKLILVARDV IRETDAFYGE LADLELQLRA APPANLYTRL GEW LLERSQ AHPDTLFAPA TPTHPEPLLY RVQALAKFAR GEEIRVEAED RQMREALDAL AR GVDAVSQ HAGPLGVMPA PAGAAPQGAP RPPPLGPEAV QVRLEEVRTQ ARRAIEGAVK E YFYRGAVY SAKALQASDN NDRRFHVASA AVVPVVQLLE SLPVFDQHTR DIAQRAAIPA PPPIATSPT AILLRDLIQR GQTLDAPEDL AAWLSVLTDA ANQGLIERKP LDELARSIR DINDQQARRS SGLAELRRFD ALDAALGQQL DSDAAFVPAP GASPYPDDGG LSPEATRM A EEALRQARAM DAAKLTAELA PDARARLRER ARSLEAMLEG ARERAKVARD AREKFLH KL QGVLRPLPDF VGLKACPAVL ATLRASLPAG WSDLPEAVRG APPEVTAALR ADMWGL LGQ YRDALEHPTP DTATALSGLH PSFVVVLKNL FADAPETPFL LQFFADHAPI IAHAV SNAI NAGSAAVATA DPASTVDAAV RAHRVLVDAV TALGAAASDP ASPLAFLAAM ADSA AGYVK ATRLALDARV AIAQLTTLGS AAADLVVQVR RAANQPEGEH ASLIQAATRA TTG ARESLA GHEGRFGGLL HAEGTAGDHS PSGRALQELG KVIGATRRRA DELEAATADL RE KMAAQRA RSSHERWAAD VEAVLDRVES GAEFDVVELR RLQALAGTHG YNPRDFRKRA E QALGTNAK AVTLALETAL AFNPYTPENQ RHPMLPPLAA IHRIDWSAAF GAAADTYADM FRVDTEPLA RLLRLAGGLL ERAQANDGFI DYHEAVLHLS EDLGGVPALR QYVPFFQKG YAEYVDIRDR LDALRADARR AIGSVALDLA AAAEEISAVR NDPAAAAELV RAGVTLPC P SEDALVACVA ALERVDQSPV KDTAYADYVA FVTRQDLADT KDAVVRAKQQ RAEATER VT AGLREVLAAR ERRAQLEAEG LANLKTLLKV VAVPATVAKT LDQARSAEEI ADQVEI LVD QTEKARELDV QAVAWLEHAQ RTFETHPLSA ASGDGPGLLT RQGARLQALF DTRRR VEAL RRSLEEAEAE WDEVWGRFGR VRGGAWKSPE GFRAACEQLR ALQDTTNTVS GLRA QRDYE RLPAKYQGVL GAKSAERAGA VEELGGRVAQ HADLSARLRD EVVPRVAWEM NFD TLGGLL AEFDAVAGDL APWAVEEFRG ARELIQRRMG LYSAYAKATG QTGAGAAAAP AP LLVDLRA LDARARASAP PGQEADPQML RRRGEAYLRV SGGPGPLVLR EATSTLDRPF A PSFLVPDG TPLQYALCFP AVTDKLGALL MCPEAACIRP PLPTDTLESA STVTAMYVLT VINRLQLAL SDAQAANFQL FGRFVRHRQA RWGASMDAAA ELYVALVATT LTREFGCRW AQLEWGGDAA APGPPLGPQS STRHRVSFNE NDVLVALVAS SPEHIYTFWR LDLVRQHE Y MHLTLPRAFQ NAADSMLFVQ RLTPHPDARI RVLPAFSAGG PPTRGLMFGT RLADWRR GK LSETDPLAPW RSVPELGTER GAALGKLSPA QALAAVSVLG RMCLPSTALV ALWTCM FPD DYTEYDSFDA LLTARLESGQ TLSPSGGREA SPPAPPNALY RPTGQHVAVP AAATH RTPA ARVTAMDLVL AAVLLGAPVV VALRNTTAFS RESELELCLT LFDSRARGPD AALR DAVSS DIETWAVRLL HADLNPIENA CLAAQLPRLS ALIAERPLAR GPPCLVLVDI SMT PVAVLW ENPDPPGPPD VRFVGSEATE ELPFVAGGED VLAASATDED PFLARAILGR PF DASLLSG ELFPGHPVYQ RAPDDQSPSV PNPTPGPVDL VGAEGSLGPG SLAPTLFTDA T PGEPVPPR MWAWIHGLEE LASDDSGGPA PLLAPDPLSP TADQSVPTSQ CAPRPPGPAV TAREARPGV PAESTRPAPV GPRDDFRRLP SPQSSPAPPD ATAPRPPASS RASAASSSG SRARRHRRAR SLARATQASA TTQGWRPPAL PDTVAPVTDF ARPPAPPKPP EPAPHALV S GVPLPLGPQA AGQASPALPI DPVPPPVATG TVLPGGENRR PPLTSGPAPT PPRVPVG GP QRRLTRPAVA SLSESRESLP SPWDPADPTA PVLGRNPAEP TSSSPAGPSP PPPAVQ PVA PPPTSGPPPT YLTLEGGVAP GGPVSRRPTT RQPVATPTTS ARPRGHLTVS RLSAP QPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQP QPQPQ PQPQPQNGHV APGEYPAVRF RAPQNRPSVP ASASSTNPRT GSSLSGVSSW ASS LALHID ATPPPVSLLQ TLYVSDDEDS DATSLFLSDS EAEALDPLPG EPHSPITNEP FS ALSADDS QEVTRLQFGP PPVSANAVLS RRYVQRTGRS ALAVLIRACY RLQQQLQRTR R ALLHHSDA VLTSLHHVRM LLG

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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 / 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..

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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: 3.0 µm / Nominal defocus min: 1.0 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

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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: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1)
Details: 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 ...Details: 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.
Number images used: 545340

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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