[English] 日本語
Yorodumi
- EMDB-31611: Cryo-EM structure of pseudorabies virus C-capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31611
TitleCryo-EM structure of pseudorabies virus C-capsid
Map data
Sample
  • Virus: Suid alphaherpesvirus 1
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: DNA packaging tegument protein UL25
    • Protein or peptide: VP1/2
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 / host cell / viral release from host cell / viral process ...chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / host cell / viral release from host cell / viral process / viral penetration into host nucleus / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / membrane => GO:0016020 / 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 / 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 large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / 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
Small capsomere-interacting protein / Major capsid protein / Triplex capsid protein 2 / Capsid vertex component 1 / VP1/2 / DNA packaging tegument protein UL25 / Triplex capsid protein 1
Similarity search - Component
Biological speciesSuid alphaherpesvirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.43 Å
AuthorsZheng Q / Li S / Zha Z / Sun H
CitationJournal: Nat Commun / Year: 2022
Title: Structures of pseudorabies virus capsids.
Authors: Guosong Wang / Zhenghui Zha / Pengfei Huang / Hui Sun / Yang Huang / Maozhou He / Tian Chen / Lina Lin / Zhenqin Chen / Zhibo Kong / Yuqiong Que / Tingting Li / Ying Gu / Hai Yu / Jun Zhang ...Authors: Guosong Wang / Zhenghui Zha / Pengfei Huang / Hui Sun / Yang Huang / Maozhou He / Tian Chen / Lina Lin / Zhenqin Chen / Zhibo Kong / Yuqiong Que / Tingting Li / Ying Gu / Hai Yu / Jun Zhang / Qingbing Zheng / Yixin Chen / Shaowei Li / Ningshao Xia /
Abstract: Pseudorabies virus (PRV) is a major etiological agent of swine infectious diseases and is responsible for significant economic losses in the swine industry. Recent data points to human viral ...Pseudorabies virus (PRV) is a major etiological agent of swine infectious diseases and is responsible for significant economic losses in the swine industry. Recent data points to human viral encephalitis caused by PRV infection, suggesting that PRV may be able to overcome the species barrier to infect humans. To date, there is no available therapeutic for PRV infection. Here, we report the near-atomic structures of the PRV A-capsid and C-capsid, and illustrate the interaction that occurs between these subunits. We show that the C-capsid portal complex is decorated with capsid-associated tegument complexes. The PRV capsid structure is highly reminiscent of other α-herpesviruses, with some additional structural features of β- and γ-herpesviruses. These results illustrate the structure of the PRV capsid and elucidate the underlying assembly mechanism at the molecular level. This knowledge may be useful for the development of oncolytic agents or specific therapeutics against this arm of the herpesvirus family.
History
DepositionAug 2, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31611.png

Downloads & links

-
Map

FileDownload / File: emd_31611.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.117 Å
Density
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-6.0271425 - 9.391193
Average (Standard dev.)0.006291551 (±0.9149454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128012801280
Spacing128012801280
CellA=B=C: 1429.76 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Suid alphaherpesvirus 1

EntireName: Suid alphaherpesvirus 1
Components
  • Virus: Suid alphaherpesvirus 1
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: DNA packaging tegument protein UL25
    • Protein or peptide: VP1/2

-
Supramolecule #1: Suid alphaherpesvirus 1

SupramoleculeName: Suid alphaherpesvirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10345 / Sci species name: Suid alphaherpesvirus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Suid alphaherpesvirus 1
Molecular weightTheoretical: 146.101984 KDa
SequenceString: MERPAILPSG QILSNIEVHS HRALFDIFKR FRSDDNNLYG AEFDALLGTY CSTLSLVRFL ELGLSVACVC TKFPELSYVA EGTIQFEVQ QPMIARDGPH PADQPVHNYM IKRLDRRSLN AAFSIAVEAL GLISGENLDG THISSAMRLR AIQQLARNVQ A VLDSFERG ...String:
MERPAILPSG QILSNIEVHS HRALFDIFKR FRSDDNNLYG AEFDALLGTY CSTLSLVRFL ELGLSVACVC TKFPELSYVA EGTIQFEVQ QPMIARDGPH PADQPVHNYM IKRLDRRSLN AAFSIAVEAL GLISGENLDG THISSAMRLR AIQQLARNVQ A VLDSFERG TADQMLRVLM EKAPPLSLLA PFTLYEGRLA DRVACAALVS ELKRRVRDDT FFLTKHERNK DAVLDRLSDL VN CTAPSVA VARMTHADTQ GRPVDGVLVT TAGVRQRLLH HVLTLADTHA DVPVTYGEMV IANTNLVTAL VMGKAVSNMD DVA RYLLGG EPAPDDGKPV GSARVRADLV VVGDRLVFLE ALEKRVYQAT QVPYPLVGNL DVTFVMPLGV FKPAADRYAR HAGS FAPTP GLPDPRTHPP RAVHFFNKDG VPCHVTFEHA MGTLCHPSFL DVDATLAALR QEPAEVQCAF GAYVADARPD ALVGL MQRF LEEWPGMMPV RPRWAAPAAA DQLLAPGNAD LRLELHPAFD FFVAPEVDVP GPFAVPQVMG QVRAMPRIIN GNIPLA LCP VDFRDARGFE LSVDRHRLAP ATVAAVRGAF RDANYPMVFY IIEAVIHGSE RTFCALARLV AQCIQSYWRN THNAAFV NN FYMVMYINTY LGNGELPEDC AAVYKDLLEH VHALRRLIGE FTLPGDPLGN QPQEELNHAL ADATLLPPLI WDCDPILY R DGLAERLPEL RVNGAHFQHI LWVEMAQVNF RNVGGGLVHN RPVRNENQPL HPHHDAEWSV LSKIYYYAVV PAFSRGNCC TMGVRYDRVY QLVQTMVVPE TDEEVGTDDP RHPLHPRNLV PNSLNVLFHN ACVAVDADAM LILQETVTNM AERTTPLLAS VAPDAGMAT VATRDMRTHD GSLHHGLLMM AYQPNDATLL EGAFFYPAPV NALFACADHL GAMRDVGAEV RAAAQHVPCV P HFLGANYY ATVRQPVAQH AAQSRADENT LSYALMAGYF KMSPVAFTHQ LRRQLHPGFA LTVVRQDRFA TENVLFAEKA SE SYFMGQM QVARTESGGG LHLQLTQPRA NVDLGVGFTA AYAAAALRAP VTDMGNLPQN LFATRGAPPM LDADADDYLR RTV NAGNRL APVPVFGQML PQVPAGLARG QQSVCEFIAT PVSVDLAYFR RACNPRGRAA GEVHGEEGLM FDHSHADPAH PHRA TANPW ASQRHSYADR LYNGQYNMSG PAYSPCFKFF TPAEAVAKSR GLARLIADTG AAASPTSNGE YQFKRPVGAG ELVED PCAL FQEAYPPLCA SDSALLRTPL GAEEHFAQYL IRDESPLKGC FQHASA

-
Macromolecule #2: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Suid alphaherpesvirus 1
Molecular weightTheoretical: 31.763766 KDa
SequenceString: MEVDIALPTL SPGDLSALQR CEGRVVFLET LRRHATLREV ALPCGGDVLA AMAAYRRRFA AVITRVTPHR MLATPLGVGG RGQSLVLQN TGPFDLTNGD HVCLVPPLLG DECLRLTSAN LELRFPMTLP LAQARELTAR VVARAAETLR GGAPARGADV V FSNGRRYQ ...String:
MEVDIALPTL SPGDLSALQR CEGRVVFLET LRRHATLREV ALPCGGDVLA AMAAYRRRFA AVITRVTPHR MLATPLGVGG RGQSLVLQN TGPFDLTNGD HVCLVPPLLG DECLRLTSAN LELRFPMTLP LAQARELTAR VVARAAETLR GGAPARGADV V FSNGRRYQ LPPPHRDNAE AATRSLVLNM IFLLNEGAVI LLSLIPNLLT LGAQDGYANA VIQLGSATRE LGQLVRQPPP PL PQDHARR FCVFEALEAW IASASRLGDT LGTRPVARVC IFDGPPTVPP GEKAAVVEV

-
Macromolecule #3: Capsid vertex component 1

MacromoleculeName: Capsid vertex component 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Suid alphaherpesvirus 1
Molecular weightTheoretical: 64.304371 KDa
SequenceString: MDAHIANETK QQMTRFAPAL VHVIVPDPLL ARAGVDPLAP FAAHAQTRYH GSGVCEPWVS VFAGHVQTGA VESVLTLPPL QRPRGPGGL FVSLPLALGA HFDGFTTAAL RVGARELVFT YDELLPARTR YNVDGERLER LCRQFANYAR ARRVAPAVAA A GGHIDALL ...String:
MDAHIANETK QQMTRFAPAL VHVIVPDPLL ARAGVDPLAP FAAHAQTRYH GSGVCEPWVS VFAGHVQTGA VESVLTLPPL QRPRGPGGL FVSLPLALGA HFDGFTTAAL RVGARELVFT YDELLPARTR YNVDGERLER LCRQFANYAR ARRVAPAVAA A GGHIDALL PPAAATIDGE AQLTRGGFDD PAAPHARDAD REILSLVRRA AELVAARHPV RSHVASGLMQ GALARRGGGG DG AGALEAA ATVPAPAARE DANGGGAAWR DELLLTPQDP RPLTALDWLD AGYAALAGGD APAHVWRRRP VSLVARRHYQ TGE TFVVVA YEHSTAWGGR RGPRGEPLAR VLAEECERHG VEHPRALPAE ARRELVRRHA ELAVPLGDEE PPLPVFDATA ELVL LERFR NACVRALLAG VRESVRREPR MRQIIEFAIR PRDREAVLDV AGRAPALLDA FARRLEHTPA REMVDSGLMT AAAAH LAAR ATAGYVTFES GPLLGGVFLF DYYSAGGEVI RVTRAPLAVA VEPATRGQFA CRFRGASHRC LPGESYAYLC VGVSRD LRA LVVLPGGFGF FATLRLEWPA ALVDPVLERL CRRV

-
Macromolecule #4: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 4 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Suid alphaherpesvirus 1
Molecular weightTheoretical: 11.509209 KDa
SequenceString:
MSFDPNNPRT ITAQTLEGAL PVDILLRLNR ATGLQMDAAE AHAIVEDARR TLFIGTSLAL VNLRRAHDKH LVERQPMFAT SDYSSWARP TVGLKRTFCP RPPP

-
Macromolecule #5: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Suid alphaherpesvirus 1
Molecular weightTheoretical: 40.008594 KDa
SequenceString: MSVQIGNGLL MVVAPGTLTV GSARARLIRQ VTLADFCEPQ AERPGLVVLA LRHPADLAGA AYAATPPGKN HRDLEEAWLA LDEGGRGLG GDGIRASVVS LNFLVAAAEN ADDALRAHVT TNYRDRRTAA RLERFATVLR AMIRSHVFPH RALHVLGGLL G HVTQDRLA ...String:
MSVQIGNGLL MVVAPGTLTV GSARARLIRQ VTLADFCEPQ AERPGLVVLA LRHPADLAGA AYAATPPGKN HRDLEEAWLA LDEGGRGLG GDGIRASVVS LNFLVAAAEN ADDALRAHVT TNYRDRRTAA RLERFATVLR AMIRSHVFPH RALHVLGGLL G HVTQDRLA SVTCVARGDQ EAARTNDMAA RRSQVHVPAC ALMDVDRELR LGGDDGLRFA YLVFVYTQRH RREALRVHVA VS RLPELGD ALSFLLAGTR VDNAIHGTDE ADAPAAPAAA AAFPAYLFND PRSARCPTGR LNTPAAEALP VWAPDMRGRA TRN SCMYAA YVRLGTVERV VRRAERCGSV DLPLAHMERF TWDVGAWEEC FF

-
Macromolecule #6: DNA packaging tegument protein UL25

MacromoleculeName: DNA packaging tegument protein UL25 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Suid alphaherpesvirus 1
Molecular weightTheoretical: 57.412797 KDa
SequenceString: MDRAWFAFEA AAIPGSARHF IAPPFPVGFW ARPGFGEGLD ARLALAHANA RRRAAAAALD NAMAAGARLE AEVDEQLRPL ERQVERVAE ALVVLEETAR AAEEADAARA AEEAPEATAA ADEGREVQIA KNDVALAYDA NLSLDFLAMV YAARGAASGV L FGTWYATL ...String:
MDRAWFAFEA AAIPGSARHF IAPPFPVGFW ARPGFGEGLD ARLALAHANA RRRAAAAALD NAMAAGARLE AEVDEQLRPL ERQVERVAE ALVVLEETAR AAEEADAARA AEEAPEATAA ADEGREVQIA KNDVALAYDA NLSLDFLAMV YAARGAASGV L FGTWYATL QATLVAERPQ VSRAIDSRDG RMSRTFMGVT TTALQACGRL YVGNRHYSAL ESAALCLHLV HRARQGPGAA GA AAPLGIA DLLERVPEYL DALSQALAEG GRISYRYNYA RVPREQLHGR YALEGHSVLA ALARLRVVPG ANVGANEVDG AGF VDEVNR AAAAFLGRGQ NLFLGEDAPL LRATVNTITG LLLLRRLLHN GNVYGDRLRN NFQLGALVPN APPPRGASGD APAS RSGDG NLRFLLAHYV VVAYRADERT ELTQLFPGLA ALALDAHSIR ARVQRHQLNL VRLVALELQN RQRVTAPVNE VIAAH DAVA VQYEEGLGLL LQQPHLRNAA DKRLGQFGVS SDYDLLYFLC LGYIPQFAAA

-
Macromolecule #7: VP1/2

MacromoleculeName: VP1/2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Suid alphaherpesvirus 1
Molecular weightTheoretical: 7.069434 KDa
SequenceString:
RVVESDTLIN RRYMRATGLG ALALLIAACR LIARRLRETR TTLKGSARRF NVDLFQVRLI LG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI F30
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: FEI FALCON III (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14252

+
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