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- EMDB-6976: Structure of the Herpes simplex virus type 2 C-capsid with capsid... -

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Basic information

Entry
Database: EMDB / ID: EMD-6976
TitleStructure of the Herpes simplex virus type 2 C-capsid with capsid-vertex-specific component
Map datafull_map
Sample
  • Virus: Human herpesvirus 2
    • Protein or peptide: VP19C
    • Protein or peptide: VP23
    • Protein or peptide: Major capsid protein
    • Protein or peptide: VP26
    • Protein or peptide: UL17
    • Protein or peptide: UL25
    • Protein or peptide: UL36
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
Major capsid protein / Large tegument protein deneddylase / Capsid vertex component 2 / Capsid vertex component 1 / Capsid triplex subunit 1 / Triplex capsid protein 2 / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman herpesvirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsWang JL / Yuan S / Zhu DJ / Tang H / Wang N / Chen WY / Gao Q / Li YH / Wang JZ / Liu HR ...Wang JL / Yuan S / Zhu DJ / Tang H / Wang N / Chen WY / Gao Q / Li YH / Wang JZ / Liu HR / Zhang XZ / Rao ZH / Wang XX
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the herpes simplex virus type 2 C-capsid with capsid-vertex-specific component.
Authors: Jialing Wang / Shuai Yuan / Dongjie Zhu / Hao Tang / Nan Wang / Wenyuan Chen / Qiang Gao / Yuhua Li / Junzhi Wang / Hongrong Liu / Xinzheng Zhang / Zihe Rao / Xiangxi Wang /
Abstract: Herpes simplex viruses (HSVs) cause human oral and genital ulcer diseases. Patients with HSV-2 have a higher risk of acquiring a human immunodeficiency virus infection. HSV-2 is a member of the α- ...Herpes simplex viruses (HSVs) cause human oral and genital ulcer diseases. Patients with HSV-2 have a higher risk of acquiring a human immunodeficiency virus infection. HSV-2 is a member of the α-herpesvirinae subfamily that together with the β- and γ-herpesvirinae subfamilies forms the Herpesviridae family. Here, we report the cryo-electron microscopy structure of the HSV-2 C-capsid with capsid-vertex-specific component (CVSC) that was determined at 3.75 Å using a block-based reconstruction strategy. We present atomic models of multiple conformers for the capsid proteins (VP5, VP23, VP19C, and VP26) and CVSC. Comparison of the HSV-2 homologs yields information about structural similarities and differences between the three herpesviruses sub-families and we identify α-herpesvirus-specific structural features. The hetero-pentameric CVSC, consisting of a UL17 monomer, a UL25 dimer and a UL36 dimer, is bound tightly by a five-helix bundle that forms extensive networks of subunit contacts with surrounding capsid proteins, which reinforce capsid stability.
History
DepositionMay 31, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseOct 10, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zz8
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6976.png

Downloads & links

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Map

FileDownload / File: emd_6976.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull_map
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-9.663976 - 16.874480999999999
Average (Standard dev.)0.00823836 (±0.7387605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120012001200
Spacing120012001200
CellA=B=C: 1656.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z120012001200
origin x/y/z0.0000.0000.000
length x/y/z1656.0001656.0001656.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120012001200
D min/max/mean-9.66416.8740.008

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Supplemental data

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Sample components

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Entire : Human herpesvirus 2

EntireName: Human herpesvirus 2
Components
  • Virus: Human herpesvirus 2
    • Protein or peptide: VP19C
    • Protein or peptide: VP23
    • Protein or peptide: Major capsid protein
    • Protein or peptide: VP26
    • Protein or peptide: UL17
    • Protein or peptide: UL25
    • Protein or peptide: UL36

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Supramolecule #1: Human herpesvirus 2

SupramoleculeName: Human herpesvirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10310 / Sci species name: Human herpesvirus 2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP19C

MacromoleculeName: VP19C / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 50.566648 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString: MKTKPLPTAP MAWAESAVET TTSPRELAGH APLRRVLRPP IARRDGPVLL GDRAPRRTAS TMWLLGIDPA ESSPGTRATR DDTEQAVDK ILRGARRAGG LTVPGAPRYH LTRQVTLTDL CQPNAERAGA LLLALRHPTD LPHLARHRAP PGRQTERLAE A WGQLLEAS ...String:
MKTKPLPTAP MAWAESAVET TTSPRELAGH APLRRVLRPP IARRDGPVLL GDRAPRRTAS TMWLLGIDPA ESSPGTRATR DDTEQAVDK ILRGARRAGG LTVPGAPRYH LTRQVTLTDL CQPNAERAGA LLLALRHPTD LPHLARHRAP PGRQTERLAE A WGQLLEAS ALGSGRAESG CARAGLVSFN FLVAACAAAY DARDAAEAVR AHITTNYGGT RAGARLDRFS ECLRAMVHTH VF PHEVMRF FGGLVSWVTQ DELASVTAVC SGPQEATHTG HPGRPRSAVT IPACAFVDLD AELCLGGPGA AFLYLVFTYR QCR DQELCC VYVVKSQLPP RGLEAALERL FGRLRITNTI HGAEDMTPPP PNRNVDFPLA VLAASSQSPR CSASQVTNPQ FVDR LYRWQ PDLRGRPTAR TCTYAAFAEL GVMPDDSPRC LHRTERFGAV GVPVVILEGV VWRPGGWRAC A

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Macromolecule #2: VP23

MacromoleculeName: VP23 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 34.373785 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString: MITDCFEADI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LALADVAHES FVSGGVSPDT LGLLLAYRRR FPAVITRVLP TRIVACPVD LGLTHAGTVN LRNTSPVDLC NGDPVSLVPP VFEGQATDVR LESLDLTLRF PVPLPTPLAR EIVARLVARG I RDLNPDPR ...String:
MITDCFEADI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LALADVAHES FVSGGVSPDT LGLLLAYRRR FPAVITRVLP TRIVACPVD LGLTHAGTVN LRNTSPVDLC NGDPVSLVPP VFEGQATDVR LESLDLTLRF PVPLPTPLAR EIVARLVARG I RDLNPDPR TPGELPDLNV LYYNGARLSL VADVQQLASV NTELRSLVLN MVYSITEGTT LILTLIPRLL ALSAQDGYVN AL LQMQSVT REAAQLIHPE APMLMQDGER RLPLYEALVA WLAHAGQLGD ILALAPAVRV CTFDGAAVVQ SGDMAPVIRY P

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Macromolecule #3: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 149.384375 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString: MAAPARDPPG YRYAAAMVPT GSILSTIEVA SHRRLFDFFA RVRSDENSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPVEQPVHNY MTKVIDRRAL NAAFSLATEA IALLTGEALD GTGISLHRQL R AIQQLARN ...String:
MAAPARDPPG YRYAAAMVPT GSILSTIEVA SHRRLFDFFA RVRSDENSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPVEQPVHNY MTKVIDRRAL NAAFSLATEA IALLTGEALD GTGISLHRQL R AIQQLARN VQAVLGAFER GTADQMLHVL LEKAPPLALL LPMQRYLDNG RLATRVARAT LVAELKRSFC DTSFFLGKAG HR REAIEAW LVDLTTATQP SVAVPRLTHA DTRGRPVDGV LVTTAAIKQR LLQSFLKVED TEADVPVTYG EMVLNGANLV TAL VMGKAV RSLDDVGRHL LEMQEEQLEA NRETLDELES APQTTRVRAD LVAIGDRLVF LEALEKRIYA ATNVPYPLVG AMDL TFVLP LGLFNPAMER FAAHAGDLVP APGHPEPRAF PPRQLFFWGK DHQVLRLSME NAVGTVCHPS LMNIDAAVGG VNHDP VEAA NPYGAYVAAP AGPGADMQQR FLNAWRQRLA HGRVRWVAEC QMTAEQFMQP DNANLALELH PAFDFFAGVA DVELPG GEV PPAGPGAIQA TWRVVNGNLP LALCPVAFRD ARGLELGVGR HAMAPATIAA VRGAFEDRSY PAVFYLLQAA IHGSEHV FC ALARLVTQCI TSYWNNTRCA AFVNDYSLVS YIVTYLGGDL PEECMAVYRD LVAHVEALAQ LVDDFTLPGP ELGGQAQA E LNHLMRDPAL LPPLVWDCDG LMRHAALDRH RDCRIDAGGH EPVYAAACNV ATADFNRNDG RLLHNTQARA ADAADDRPH RPADWTVHHK IYYYVLVPAF SRGRCCTAGV RFDRVYATLQ NMVVPEIAPG EECPSDPVTD PAHPLHPANL VANTVNAMFH NGRVVVDGP AMLTLQVLAH NMAERTTALL CSAAPDAGAN TASTANMRIF DGALHAGVLL MAPQHLDHTI QNGEYFYVLP V HALFAGAD HVANAPNFPP ALRDLARHVP LVPPALGANY FSSIRQPVVQ HARESAAGEN ALTYALMAGY FKMSPVALYH QL KTGLHPG FGFTVVRQDR FVTENVLFSE RASEAYFLGQ LQVARHETGG GVNFTLTQPR GNVDLGVGYT AVAATATVRN PVT DMGNLP QNFYLGRGAP PLLDNAAAVY LRNAVVAGNR LGPAQPLPVF GCAQVPRRAG MDHGQDAVCE FIATPVATDI NYFR RPCNP RGRAAGGVYA GDKEGDVIAL MYDHGQSDPA RPFAATANPW ASQRFSYGDL LYNGAYHLNG ASPVLSPCFK FFTAA DITA KHRCLERLIV ETGSAVSTAT AASDVQFKRP PGCRELVEDP CGLFQEAYPI TCASDPALLR SARDGEAHAR ETHFTQ YLI YDASPLKGLS L

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Macromolecule #4: VP26

MacromoleculeName: VP26 / type: protein_or_peptide / ID: 4 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 12.147707 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString:
MAAPQFHRPS TITADNVRAL GMRGLVLATN NAQFIMDNSY PHPHGTQGAV REFLRGQAAA LTDLGVTHAN NTFAPQPMFA GDAAAEWLR PSFGLKRTYS PFVVRDPKTP STP

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Macromolecule #5: UL17

MacromoleculeName: UL17 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 74.747805 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString: MNAHFANEVQ YDLTRDPSSP ASLIHVIISS ECLAAAGVPL SALVRGRPDG GAAANFRVET QTRAHATGDC TPWRSAFAAY VPADAVGAI LAPVIPAHPD LLPRVPSAGG LFVSLPVACD AQGVYDPYTV AALRLAWGPW ATCARVLLFS YDELVPPNTR Y AADGARLM ...String:
MNAHFANEVQ YDLTRDPSSP ASLIHVIISS ECLAAAGVPL SALVRGRPDG GAAANFRVET QTRAHATGDC TPWRSAFAAY VPADAVGAI LAPVIPAHPD LLPRVPSAGG LFVSLPVACD AQGVYDPYTV AALRLAWGPW ATCARVLLFS YDELVPPNTR Y AADGARLM RLCRHFCRYV ARLGAAAPAA ATEAAAHLSL GMGESGTPTP QASSVSGGAG PAVVGTPDPP ISPEEQLTAP GG DTATAED VSITQENEEI LALVQRAVQD VTRRHPVRAR PKHAASGVAS GLRQGALVHQ AVSGGALGAS DAEAVLAGLE PPG GGRFAT PGGPRAAGED VLNDVLTLVP GTAKPRSLVE WLDRGWEALA GGDRPDWLWS RRSISVVLRH HYGTKQRFVV VSYE NSVAW GGRRARPPRL SSELATALTE ACAAERVVRP HQLSPAAQTA LLRRFPALEG PLRHPRPVLQ PFDIAAEVAF VARIQ IACL RALGHSIRAA LQGGPRIFQR LRYDFGPHQS EWLGEVTRRF PVLLENLMRA LEGTAPDAFF HTAYALAVLA HLGGQG GRG RRRRLVPLSD DIPARFADSD AHYAFDYYST SGDTLRLTNR PIAVVIDGDV NGREQSKCRF MEGSPSTAPH RVCEQYL PG ESYAYLCLGF NRRLCGLVVF PGGFAFTINT AAYLSLADPV ARAVGLRFCR GAATGPGLVR

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Macromolecule #6: UL25

MacromoleculeName: UL25 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 63.623836 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString: MDPYYPFDAL DVWEHRRFIV ADSRSFITPE FPRDFWMLPV FNIPRETAAE RAAVLQAQRT AAAAALENAA LQAAELPVDI ERRIRPIEQ QVHHIADALE ALETAAAAAE EADAARDAEA RGEGAADGAA PSPTAGPAAA EMEVQIVRND PPLRYDTNLP V DLLHMVYA ...String:
MDPYYPFDAL DVWEHRRFIV ADSRSFITPE FPRDFWMLPV FNIPRETAAE RAAVLQAQRT AAAAALENAA LQAAELPVDI ERRIRPIEQ QVHHIADALE ALETAAAAAE EADAARDAEA RGEGAADGAA PSPTAGPAAA EMEVQIVRND PPLRYDTNLP V DLLHMVYA GRGAAGSSGV VFGTWYRTIQ ERTIADFPLT TRSADFRDGR MSKTFMTALV LSLQSCGRLY VGQRHYSAFE CA VLCLYLL YRTTHESSPD RDRAPVAFGD LLARLPRYLA RLAAVIGDES GRPQYRYRDD KLPKAQFAAA GGRYEHGALA THV VIATLV RHGVLPAAPG DVPRDTSTRV NPDDVAHRDD VNRAAAAFLA RGHNLFLWED QTLLRATANT ITALAVLRRL LANG NVYAD RLDNRLQLGM LIPGAVPAEA IARGASGLDS GAIKSGDNNL EALCVNYVLP LYQADPTVEL TQLFPGLAAL CLDAQ AGRP LASTRRVVDM SSGARQAALV RLTALELINR TRTNTTPVGE IINAHDALGI QYEQGLGLLA QQARIGLASN AKRFAT FNV GSDYDLLYFL CLGFIPQYLS VA

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Macromolecule #7: UL36

MacromoleculeName: UL36 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 330.616156 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString: MIPAALPHPT MKRQGDRDIV VTGVRNQFAT DLEPGGSVSC MRSSLSFLSL LFDVGPRDVL SAEAIEGCLV EGGEWTRAAA GSGPPRMCS IIELPNFLEY PAARGGLRCV FSRVYGEVGF FGEPTAGLLE TQCPAHTFFA GPWAMRPLSY TLLTIGPLGM G LYRDGDTA ...String:
MIPAALPHPT MKRQGDRDIV VTGVRNQFAT DLEPGGSVSC MRSSLSFLSL LFDVGPRDVL SAEAIEGCLV EGGEWTRAAA GSGPPRMCS IIELPNFLEY PAARGGLRCV FSRVYGEVGF FGEPTAGLLE TQCPAHTFFA GPWAMRPLSY TLLTIGPLGM G LYRDGDTA YLFDPHGLPA GTPAFIAKVR AGDVYPYLTY YAHDRPKVRW AGAMVFFVPS GPGAVAPADL TAAALHLYGA SE TYLQDEP FVERRVAITH PLRGEIGGLG ALFVGVVPRG DGEGSGPVVP ALPAPTHVQT PRADRPPEAP RGASGPPDTP QAG HPNRPP DDVWAAALEG TPPAKPSAPD AAASGPPHAA PPPQTPAGDA AEEAEDLRVL EVGAVPVGRH RARYSTGLPK RRRP TWTPP SSVEDLTSGE RPAPKAPPAK AKKKSAPKKK APVAAEVPAS SPTPIAATVP PAPDTPPQSG QGGGDDGPAS PSSPS VLET LGARRPPEPP GADLAQLFEV HPNVAATAVR LAARDAALAR EVAACSQLTI NALRSPYPAH PGLLELCVIF FFERVL AFL IENGARTHTQ AGVAGPAAAL LDFTLRMLPR KTAVGDFLAS TRMSLADVAA HRPLIQHLLD ENSQIGRLAL AKLVLVA RD VIRETDAFYG DLADLDLQLR AAPPANLYAR LGEWLLERSR AHPNTLFAPA TPTHPEPLLH RIQALAQFAR GEEMRVEA E AREMREALDA LARGVDSVSQ RAGPLTVMPV PAAPGAGGRA PCPPALGPEA IQARLEDVRI QARRAIESAI KEYFHRGAV YSAKALQASD SHDCRFHVAS AAVVPMVQLL ESLPAFDQHT RDVAQRAALP PPPPLATSPQ AILLRDLLQR GQTLDAPEDL AAWLSVLTD AATQGLIERK PLEELARSIH GINDQQARRS SGLAELQRFD ALDAALAQQL DSDAAFVPAT GPAPYVDGGG L SPEATRMA EDALRQARAM EAAKMTAELA PEARSRLRER AHALEAMLND ARERAKVAHD AREKFLHKLQ GVLRPLPDFV GL KACPAVL ATLRASLPAG WTDLADAVRG PPPEVTAALR ADLWGLLGQY REALEHPTPD TATALAGLHP AFVVVLKTLF ADA PETPVL VQFFSDHAPT IAKAVSNAIN AGSAAVATAS PAATVDAAVR AHGALADAVS ALGAAARDPA SPLSFLAALA DSAA GYVKA TRLALEARGA IDELTTLGSA AADLVVQARR ACAQPEGDHA ALIDAAARAT TAARESLAGH EAGFGGLLHA EGTAG DHSP SGRALQELGK VIGATRRRAD ELEAAVADLT AKMAAQRARG SSERWAAGVE AALDRVENRA EFDVVELRRL QALAGT HGY NPRDFRKRAE QALAANAEAV TLALDTAFAF NPYTPENQRH PMLPPLAAIH RLGWSAAFHA AAETYADMFR VDAEPLA RL LRIAEGLLEM AQAGDGFIDY HEAVGRLADD MTSVPGLRRY VPFFQHGYAD YVELRDRLDA IRADVHRALG GVPLDLAA A AEQISAARND PEATAELVRT GVTLPCPSED ALVACAAALE RVDQSPVKNT AYAEYVAFVT RQDTAETKDA VVRAKQQRA EATERVMAGL REALAARERR AQIEAEGLAN LKTMLKVVAV PATVAKTLDQ ARSVAEIADQ VEVLLDQTEK TRELDVPAVI WLEHAQRTF ETHPLSAARG DGPGPLARHA GRLGALFDTR RRVDALRRSL EEAEAEWDEV WGRFGRVRGG AWKSPEGFRA M HEQLRALQ DTTNTVSGLR AQPAYERLSA RYQGVLGAKG AERAEAVEEL GARVTKHTAL CARLRDEVVR RVPWEMNFDA LG RLLAEFD AAAADLAPWA VEEFRGAREL IQYRMGLYSA YARAGGQTGA GAESAPAPLL VDLRALDARA RASSSPEGHE VDP QLLRRR GEAYLRAGGD PGPLVLREAV SALDLPFATS FLAPDGTPLQ YALCFPAVTD KLGALLMRPE AACVRPPLPT DVLE SAPTV TAMYVLTVVN RLQLALSDAQ AANFQLFGRF VRHRQATWGA SMDAAAELYV ALVATTLTRE FGCRWAQLGW ASGAA APRP PPGPRGSQRH CVAFNENDVL VALVAGVPEH IYNFWRLDLV RQHEYMHLTL ERAFEDAAES MLFIQRLTPH PDARIR VLP TFLDGGPPTR GLLFGTRLAD WRRGKLSETD PLAPWRSALE LGTQRRDAPA LGKLSPAQAL AAVSVLGRMC LPSAALA AL WTCMFPDDYT EYDSFDALLA ARLESGQTLG PAGGREASLP EAPHALYRPT GQHVAVLAAA THRTPAARVT AMDLVLAA V LLGAPVVVAL RNTTAFSRES ELELCLTLFD SRPGGPDAAL RDVVSSDIET WAVGLLHTDL NPIENACLAA QLPRLSALI AERPLADGPP CLVLVDISMT PVAVLWEAPE PPGPPDVRFV GSEATEELPF VATAGDVLAA SAADADPFFA RAILGRPFDA SLLTGELFP GHPVYQRPLA DEAGPSAPTA ARDPRDLAGG DGGSGPEDPA APPARQADPG VLAPTLLTDA TTGEPVPPRM W AWIHGLEE LASDDAGGPT PNPAPALLPP PATDQSVPTS QYAPRPIGPA ATARETRPSV PPQQNTGRVP VAPRDDPRPS PP TPSPPAD AALPPPAFSG SAAAFSAAVP RVRRSRRTRA KSRAPRASAP PEGWRPPALP APVAPVAASA RPPDQPPTPE SAP PAWVSA LPLPPGPASA RGAFPAPTLA PIPPPPAEGA VVPGGDRRRG RRQTTAGPSP TPPRGPAAGP PRRLTRPAVA SLSA SLNSL PSPRDPADHA AAVSAAAAAV PPSPGLAPPT SAVQTSPPPL APGPVAPSEP LCGWVVPGGP VARRPPPQSP ATKPA ARTR IRARSVPQPP LPQPPLPQPP LPQPPLPQPP LPQPPLPQPP LPQPPLPQPP LPQPPLPQPP LPPVTRTLTP QSRDSV PTP ESPTHTNTHL PVSAVTSWAS SLALHVDSAP PPASLLQTLH ISSDDEHSDA DSLRFSDSDD TEALDPLPPE PHLPPAD EP PGPLAADHLQ SPHSQFGPLP VQANAVLSRR YVRSTGRSAL AVLIRACRRI QQQLQRTRRA LFQRSNAVLT SLHHVRML L G

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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
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: OTHER
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56901

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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

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