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- EMDB-31298: C5 portal vertex in the partially-enveloped virion capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-31298
TitleC5 portal vertex in the partially-enveloped virion capsid
Map data
Sample
  • Virus: Human betaherpesvirus 5
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Large tegument protein deneddylase
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: ORFL92C_UL32
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Major capsid protein
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm ...T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / cysteine-type deubiquitinase activity / host cell nucleus / structural molecule activity / proteolysis / DNA binding
Similarity search - Function
Herpesvirus UL11/UL32 / Small capsid protein, Herpesviridae / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein of Herpesviridae / 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 UL11/UL32 / Small capsid protein, Herpesviridae / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein of Herpesviridae / 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 / UL77 protein / UL48 protein / Capsid vertex component 1 / ORFL92C_UL32 / Small capsomere-interacting protein / Capsid triplex subunit 2 / Capsid triplex subunit 1
Similarity search - Component
Biological speciesHHV-5, Human herpesvirus 5 / Human betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLi Z / Yu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for genome packaging, retention, and ejection in human cytomegalovirus.
Authors: Zhihai Li / Jingjing Pang / Lili Dong / Xuekui Yu /
Abstract: How the human cytomegalovirus (HCMV) genome-the largest among human herpesviruses-is packaged, retained, and ejected remains unclear. We present the in situ structures of the symmetry-mismatched ...How the human cytomegalovirus (HCMV) genome-the largest among human herpesviruses-is packaged, retained, and ejected remains unclear. We present the in situ structures of the symmetry-mismatched portal and the capsid vertex-specific components (CVSCs) of HCMV. The 5-fold symmetric 10-helix anchor-uncommon among known portals-contacts the portal-encircling DNA, which is presumed to squeeze the portal as the genome packaging proceeds. We surmise that the 10-helix anchor dampens this action to delay the portal reaching a "head-full" packaging state, thus facilitating the large genome to be packaged. The 6-fold symmetric turret, latched via a coiled coil to a helix from a major capsid protein, supports the portal to retain the packaged genome. CVSCs at the penton vertices-presumed to increase inner capsid pressure-display a low stoichiometry, which would aid genome retention. We also demonstrate that the portal and capsid undergo conformational changes to facilitate genome ejection after viral cell entry.
History
DepositionMay 13, 2021-
Header (metadata) releaseJul 14, 2021-
Map releaseJul 14, 2021-
UpdateAug 18, 2021-
Current statusAug 18, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7etj
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7etj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31298.png

Downloads & links

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Map

FileDownload / File: emd_31298.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.625 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.02
Minimum - Maximum-0.06822433 - 0.09250568
Average (Standard dev.)0.005121377 (±0.008799275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6251.6251.625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0680.0930.005

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Supplemental data

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Sample components

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Entire : Human betaherpesvirus 5

EntireName: Human betaherpesvirus 5
Components
  • Virus: Human betaherpesvirus 5
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Large tegument protein deneddylase
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: ORFL92C_UL32
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Human betaherpesvirus 5

SupramoleculeName: Human betaherpesvirus 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10359 / Sci species name: Human betaherpesvirus 5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: HHV-5, Human herpesvirus 5
Molecular weightTheoretical: 34.63575 KDa
SequenceString: MAAMEANIFC TFDHKLSIAD VGKLTKLVAA VVPIPQRLHL IKHYQLGLHQ FVDHTRGYVR LRGLLRNMTL TLMRRVEGNQ ILLHVPTHG LLYTVLNTGP VTWEKGDALC VLPPLFHGPL ARENLLTLGQ WELVLPWIVP MPLALEINQR LLIMGLFSLD R SYEEVKAA ...String:
MAAMEANIFC TFDHKLSIAD VGKLTKLVAA VVPIPQRLHL IKHYQLGLHQ FVDHTRGYVR LRGLLRNMTL TLMRRVEGNQ ILLHVPTHG LLYTVLNTGP VTWEKGDALC VLPPLFHGPL ARENLLTLGQ WELVLPWIVP MPLALEINQR LLIMGLFSLD R SYEEVKAA VQQLQTITFR DATFTIPDPV IDQHLLIDMK TACLSMSMVA NLASELTMTY VRKLALEDSS MLLVKCQELL MR LDRERSV GEPRTPARPQ HVSPDDEIAR LSALFVMLRQ LDDLIREQVV FTVCDVSPDN KSATCIFKG

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Macromolecule #2: Large tegument protein deneddylase

MacromoleculeName: Large tegument protein deneddylase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: HHV-5, Human herpesvirus 5
Molecular weightTheoretical: 253.541141 KDa
SequenceString: MKVTQASCHQ GDIARFGARA GNQCVCNGIM FLHALHLGGT SAVLQTEALD AIMEEGARLD ARLERELQKK LPAGGRLPVY RLGDEVPRR LESRFGRTVH ALSRPFNGTT ETCDLDGYMC PGIFDFLRYA HAKPRPTYVL VTVNSLARAV VFTEDHMLVF D PHSSAECH ...String:
MKVTQASCHQ GDIARFGARA GNQCVCNGIM FLHALHLGGT SAVLQTEALD AIMEEGARLD ARLERELQKK LPAGGRLPVY RLGDEVPRR LESRFGRTVH ALSRPFNGTT ETCDLDGYMC PGIFDFLRYA HAKPRPTYVL VTVNSLARAV VFTEDHMLVF D PHSSAECH NAAVYHCEGL HQVLMVLTGF GVQLSPAFYY EALFLYMLDV ATVPEAEIAA RLVSTYRDRD IDLTGVVRES AD TAATTTT AAPSLPPLPD PIVDPGCPPG VAPSIPVYDP SSSPKKTPEK RRKDLSGSKH GGKKKPPSTT SKTLATASSS PSA IAAASS SSAVPPSYSC GEGALPALGR YQQLVDEVEQ ELKALTLPPL PANTSAWTLH AAGTESGANA ATATAPSFDE AFLT DRLQQ LIIHAVNQRS CLRRPCGPQS AAQQAVRAYL GLSKKLDAFL LNWLHHGLDL QRMHDYLSHK TTKGTYSTLD RALLE KMQV VFDPYGRQHG PALIAWVEEM LRYVESKPTN ELSQRLQRFV TKRPMPVSDS FVCLRPVDFQ RLTQVIEQRR RVLQRQ REE YHGVYEHLAG LITSIDIHDL DASDLNRREI LKALQPLDDN AKQELFRLGN AKMLELQMDL DRLSTQLLTR VHNHILN GF LPVEDLKQME RVVEQVLRLF YDLRDLKLCD GSYEEGFVVI REQLSYLMTG TVRDNVPLLQ EILQLRHAYQ QATQQNEG R LTQIHDLLHV IETLVRDPGS RGSALTLALV QEQLAQLEAL GGLQLPEVQQ RLQNAQLALS RLYEEEEETQ RFLDGLSYD DPPNEQTIKR HPQLREMLRR DEQTRLRLIN AVLSMFHTLV MRLARDESPR PTFFDAVSLL LQQLPPDSHE REDLRAANAT YAQMVKKLE QIEKAGTGAS EKRFQALREL VYFFRNHEYF FQHMVGRLGV GPQVTELYER YQHEMEEQHL ERLEREWQEE A GKLTVTSV EDVQRVLARA PSHRVMHQMQ QTLTTKMQDF LDKEKRKQEE QQRQLLDGYQ KKVQQDLQRV VDAVKGEMLS TI PHQPLEA TLELLLGLDQ RAQPLLDKFN QDLLSALQQL SKKLDGRINE CLHGVLTGDV ERRCHPHREA AMQTQASLNH LDQ ILGPQL LIHETQQALQ HAVHQAQFIE KCQQGDPTTA ITGSEFEGDF ARYRSSQQKM EEQLQETRQQ MTETSERLDR SLRQ DPGSS SVTRVPEKPF KGQELAGRIT PPPADFQQPV FKTLLDQQAD AARKALSDEA DLLNQKVQTQ LRQRDEQLST AQNLW TDLV TRHKMSGGLD VTTPDAKALM EKPLETLREL LGKATQQLPY LSAERTVRWM LAFLEEALAQ ITADPTHPHH GSRTHY RNL QQQAVESAVT LAHQIEQNAA CENFIAQHQE ATANGASTPR VDMVQAVEAV WQRLEPGRVA GGAARHQKVQ ELLQRLG QT LGDLELQETL ATEYFALLHG IQTFSYGLDF RSQLEKIRDL RTRFAELAKR RGTRLSNEGV LPNPRKPQAT TSLGAFTR G LNALERHVQL GHQYLLNKLN GSSLVYRLED IPSVLPATHE TDPALIMRDR LRRLCFARHH DTFLEVVDVF GMRQIVTQA GEPIHLVTDY GNVAFKYLAL RDDGRPLAWR RRCSGGGLKN VVTTRYKAIT VAVAVCQTLR TFWPQISQYD LRPYLTQHQS HTHPAETHT LHNLKLFCYL VSTAWHQRID TQQELTAADR VGSGEGGDVG EQRPGRGTVL RLSLQEFCVL IAALYPEYIY T VLKYPVQM SLPSLTAHLH QDVIHAVVNN THKMPPDHLP EQVKAFCITP TQWPAMQLNK LFWENKLVQQ LCQVGPQKST PP LGKLWLY AMATLVFPQD MLQCLWLELK PQYAETYASV SELVQTLFQI FTQQCEMVTE GYTQPQLPTG EPVLQMIRVP RQD TTTTDT NTTTEPGLLD VFIQTETALD YALGSWLFGI PVCLGVHVAD LLKGQRILVA RHLEYTSRDR DFLRIQRSRD LNLS QLLQD TWTETPLEHC WLQAQIRRLR DYLRFPTRLE FIPLVIYNAQ DHTVVRVLRP PSTFEQDHSR LVLDEAFPTF PLYDQ DDNS SADNIAASGA APTPPVPFNR VPVNIQFLRE NPPPIARVQQ PPRRHRHRAA AAADDDGQID HVQDDTSRTA DSALVS TAF GGSVFQENRL GETPLCRDEL VAVAPGAAST SFASPPITVL TQNVLSALEI LRLVRLDLRQ LAQSVQDTIQ HMRFLYL L

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Macromolecule #3: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HHV-5, Human herpesvirus 5
Molecular weightTheoretical: 33.07127 KDa
SequenceString: MDARAVAKRP RDPADEDNEL VTALKAKREV NTISVRYLYH ADHQALTARF FVPEGLVEFE AQPGALLIRM ETGCDSPRHL YISLYLLGI RASNVSASTR CLLESVYTAS AARAALQWLD LGPHLLHRRL ETLGCVKTVS LGITSLLTCV MRGYLYNTLK T EVFALMIP ...String:
MDARAVAKRP RDPADEDNEL VTALKAKREV NTISVRYLYH ADHQALTARF FVPEGLVEFE AQPGALLIRM ETGCDSPRHL YISLYLLGI RASNVSASTR CLLESVYTAS AARAALQWLD LGPHLLHRRL ETLGCVKTVS LGITSLLTCV MRGYLYNTLK T EVFALMIP KDMYLTWEET RGRLQYVYLI IVYDYDGPET RPGIYVLTSS IAHWQTLVDV ARGKFARERC SFVNRRITRP RQ IPLCTGV IQKLGWCLAD DIHTSFLVHK ELKLSVVRLD NFSVELGDFR EFV

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Macromolecule #4: Capsid vertex component 1

MacromoleculeName: Capsid vertex component 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HHV-5, Human herpesvirus 5
Molecular weightTheoretical: 68.567211 KDa
SequenceString: METHLYSDLA FEARFADDEQ LPLHLVLDQE VLSNEEAETL RYVYYRNVDS AGRSTGRAPG GDEDDAPASD DAEDAVGGDR AFDRERRTW QRACFRVLPR PLELLDYLRQ SGLTVTLEKE QRVRMFYAVF TTLGLRCPDN RLSGAQTLHL RLVWPDGSYR D WEFLARDL ...String:
METHLYSDLA FEARFADDEQ LPLHLVLDQE VLSNEEAETL RYVYYRNVDS AGRSTGRAPG GDEDDAPASD DAEDAVGGDR AFDRERRTW QRACFRVLPR PLELLDYLRQ SGLTVTLEKE QRVRMFYAVF TTLGLRCPDN RLSGAQTLHL RLVWPDGSYR D WEFLARDL LREEMEANKR DRQHQLATTT NHRRRGGLRN NLDNGSDRRL PEAAVASLET AVSTPFFEIP NGAGTSSANG DG RFSNLEQ RVARLLRGDE EFIYHAGPLE PPSKIRGHEL VQLRLDVNPD LMYATDPHDR DEVARTDEWK GAGVSRLREV WDV QHRVRL RVLWYVNSFW RSRELSYDDH EVELYRALDA YRARIAVEYV LIRAVRDEIY AVLRRDGGAL PQRFACHVSR NMSW RVVWE LCRHALALWM DWADVRSCII KALTPRLSRG AAAAAQRARR QRERSAPKPQ ELLFGPRNES GPPAEQTWYA DVVRC VRAQ VDLGVEVRAA RCPRTGLWIV RDRRGRLRRW LSQPEVCVLY VTPDLDFYWV LPGGFAVSSR VTLHGLAQRA LRDRFQ NFE AVLARGMHVE AGRQEPETPR VSGRRLPFDD L

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Macromolecule #5: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HHV-5, Human herpesvirus 5
Molecular weightTheoretical: 71.26957 KDa
SequenceString: MSLLHTFWRL PVAVFFEPHE ENVLRCPERV LRRLLEDAAV TMRGGGWRED VLMDRVRKRY LRQELRDLGH RVQTYCEDLE GRVSEAEAL LNQQCELDEG PSPRTLLQPP CRPRSSSPGT GVAGASAVPH GLYSRHDAIT GPAAAPSDVV APSDAVAASA A AGASSTWL ...String:
MSLLHTFWRL PVAVFFEPHE ENVLRCPERV LRRLLEDAAV TMRGGGWRED VLMDRVRKRY LRQELRDLGH RVQTYCEDLE GRVSEAEAL LNQQCELDEG PSPRTLLQPP CRPRSSSPGT GVAGASAVPH GLYSRHDAIT GPAAAPSDVV APSDAVAASA A AGASSTWL AQCAERPLPG NVPSYFGITQ NDPFIRFHTD FRGEVVNTMF ENASTWTFSF GIWYYRLKRG LYTQPRWKRV YH LAQMDNF SISQELLLGV VNALENVTVY PTYDCVLSDL EAAACLLAAY GHALWEGRDP PDSVATVLGE LPQLLPRLAD DVS REIAAW EGPVAAGNNY YAYRDSPDLR YYMPLSGGRH YHPGTFDRHV LVRLFHKRGV IQHLPGYGTI TEELVQERLS GQVR DDVLS LWSRRLLVGK LGRDVPVFVH EQQYLRSGLT CLAGLLLLWK VTNADSVFAP RTGKFTLADL LGSDAVAGGG LPGGR AGGE EEGYGGRHGR VRNFEFLVRY YIGPWYARDP AVTLSQLFPG LALLAVTESV RSGWDPSRRE DSAGGGDGGG AVLMQL SKS NPVADYMFAQ SSKQYGDLRR LEVHDALLFH YEHGLGRLLS VTLPRHRVST LGSSLFNVND IYELLYFLVL GFLPSVA VL

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Macromolecule #6: ORFL92C_UL32

MacromoleculeName: ORFL92C_UL32 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HHV-5, Human herpesvirus 5
Molecular weightTheoretical: 112.829102 KDa
SequenceString: MSLQFIGLQR RDVVALVNFL RHLTQKPDVD LEAHPKILKK CGEKRLHRRT VLFNELMLWL GYYRELRFHN PDLSSVLEEF EVRCVAVAR RGYTYPFGDR GKARDHLAVL DRTEFDTDVR HDAEIVERAL VSAVILAKMS VRETLVTAIG QTEPIAFVHL K DTEVQRIE ...String:
MSLQFIGLQR RDVVALVNFL RHLTQKPDVD LEAHPKILKK CGEKRLHRRT VLFNELMLWL GYYRELRFHN PDLSSVLEEF EVRCVAVAR RGYTYPFGDR GKARDHLAVL DRTEFDTDVR HDAEIVERAL VSAVILAKMS VRETLVTAIG QTEPIAFVHL K DTEVQRIE ENLEGVRRNM FCVKPLDLNL DRHANTALVN AVNKLVYTGR LIMNVRRSWE ELERKCLARI QERCKLLVKE LR MCLSFDS NYCRNILKHA VENGDSADTL LELLIEDFDI YVDSFPQSAH TFLGARSPSL EFDDDANLLS LGGGSAFSSV PKK HVPTQP LDGWSWIASP WKGHKPFRFE AHGSLAPAAE AHAARSAAVG YYDEEEKRRE RQKRVDDEVV QREKQQLKAW EERQ QNLQQ RQQQPPPPAR KPSASRRLFG SSADEDDDDD DDEKNIFTPI KKPGTSGKGA ASGGGVSSIF SGLLSSGSQK PTSGP LNIP QQQQRHAAFS LVSPQVTKAS PGRVRRDSAW DVRPLTETRG DLFSGDEDSD SSDGYPPNRQ DPRFTDTLVD ITDTET SAK PPVTTAYKFE QPTLTFGAGV NVPAGAGAAI LTPTPVNPST APAPAPTPTF AGTQTPVNGN SPWAPTAPLP GDMNPAN WP RERAWALKNP HLAYNPFRMP TTSTASQNTV STTPRRPSTP RAAVTQTASR DAADEVWALR DQTAESPVED SEEEDDDS S DTGSVVSLGH TTPSSDYNND VISPPSQTPE QSTPSRIRKA KLSSPMTTTS TSQKPVLGKR VATPHASARA QTVTSTPVQ GRLEKQVSGT PSTVPATLLQ PQPASSKTTS SRNVTSGAGT SSASSARQPS ASASVLSPTE DDVVSPATSP LSMLSSASPS PAKSAPPSP VKGRGSRVGV PSLKPTLGGK AVVGRPPSVP VSGSAPGRLS GSSRAASTTP TYPAVTTVYP PSSTAKSSVS N APPVASPS ILKPGASAAL QSRRSTGTAA VGSPVKSTTG MKTVAFDLSS PQKSGTGPQP GSAGMGGAKT PSDAVQNILQ KI EKIKNTE E

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Macromolecule #7: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 7 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: HHV-5, Human herpesvirus 5
Molecular weightTheoretical: 8.495924 KDa
SequenceString:
MSNTAPGPTV ANKRDEKHRH VVNVVLELPT EISEATHPVL ATMLSKYTRM SSLFNDKCAF KLDLLRMVAV SRTRR

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Macromolecule #8: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: HHV-5, Human herpesvirus 5
Molecular weightTheoretical: 154.048906 KDa
SequenceString: MENWSALELL PKVGIPTDFL THVKTSAGEE MFEALRIYYG DDPERYNIHF EAIFGTFCNR LEWVYFLTSG LAAAAHAIKF HDLNKLTTG KMLFHVQVPR VASGAGLPTS RQTTIMVTKY SEKSPITIPF ELSAACLTYL RETFEGTILD KILNVEAMHT V LRALKNTA ...String:
MENWSALELL PKVGIPTDFL THVKTSAGEE MFEALRIYYG DDPERYNIHF EAIFGTFCNR LEWVYFLTSG LAAAAHAIKF HDLNKLTTG KMLFHVQVPR VASGAGLPTS RQTTIMVTKY SEKSPITIPF ELSAACLTYL RETFEGTILD KILNVEAMHT V LRALKNTA DAMERGLIHS FLQTLLRKAP PYFVVQTLVE NATLARQALN RIQRSNILQS FKAKMLATLF LLNRTRDRDY VL KFLTRLA EAATDSILDN PTTYTTSSGA KISGVMVSTA NVMQIIMSLL SSHITKETVS APATYGNFVL SPENAVTAIS YHS ILADFN SYKAHLTSGQ PHLPNDSLSQ AGAHSLTPLS MDVIRLGEKT VIMENLRRVY KNTDTKDPLE RNVDLTFFFP VGLY LPEDR GYTTVESKVK LNDTVRNALP TTAYLLNRDR AVQKIDFVDA LKTLCHPVLH EPAPCLQTFT ERGPPSEPAM QRLLE CRFQ QEPMGGAARR IPHFYRVRRE VPRTVNEMKQ DFVVTDFYKV GNITLYTELH PFFDFTHCQE NSETVALCTP RIVIGN LPD GLAPGPFHEL RTWEIMEHMR LRPPPDYEET LRLFKTTVTS PNYPELCYLV DVLVHGNVDA FLLIRTFVAR CIVNMFH TR QLLVFAHSYA LVTLIAEHLA DGALPPQLLF HYRNLVAVLR LVTRISALPG LNNGQLAEEP LSAYVNALHD HRLWPPFV T HLPRNMEGVQ VVADRQPLNP ANIEARHHGV SDVPRLGAMD ADEPLFVDDY RATDDEWTLQ KVFYLCLMPA MTNNRACGL GLNLKTLLVD LFYRPAFLLM PAATAVSTSG TTSKESTSGV TPEDSIAAQR QAVGEMLTEL VEDVATDAHT PLLQACRELF LAVQFVGEH VKVLEVRAPL DHAQRQGLPD FISRQHVLYN GCCVVTAPKT LIEYSLPVPF HRFYSNPTIC AALSDDIKRY V TEFPHYHR HDGGFPLPTA FAHEYHNWLR SPFSRYSATC PNVLHSVMTL AAMLYKISPV SLVLQTKAHI HPGFALTAVR TD TFEVDML LYSGKSCTSV IINNPIVTKE ERDISTTYHV TQNINTVDMG LGYTSNTCVA YVNRVRTDMG VRVQDLFRVF PMN VYRHDE VDRWIRHAAG VERPQLLDTE TISMLTFGSM SERNAAATVH GQKAACELIL TPVTMDVNYF KIPNNPRGRA SCML AVDPY DTEAATKAIY DHREADAQTF AATHNPWASQ AGCLSDVLYN TRHRERLGYN SKFYSPCAQY FNTEEIIAAN KTLFK TIDE YLLRAKDCIR GDTDTQYVCV EGTEQLIENP CRLTQEALPI LSTTTLALME TKLKGGAGAF ATSETHFGNY VVGEII PLQ QSMLFNS

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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: 7.5
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 K3 BIOQUANTUM (6k 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 reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42849

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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

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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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