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- EMDB-31612: Cryo-EM structure of PRV A-capid -

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Basic information

Entry
Database: EMDB / ID: EMD-31612
TitleCryo-EM structure of PRV A-capid
Map data
SampleCryo-EM structure of PRV A-capsid != Suid alphaherpesvirus 1

Cryo-EM structure of PRV A-capsid

  • Virus: Suid alphaherpesvirus 1
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Small capsomere-interacting protein
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus UL35 / Herpesvirus UL35 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
Similarity search - Domain/homology
Small capsomere-interacting protein / Major capsid protein / Triplex capsid protein 2 / Triplex capsid protein 1
Similarity search - Component
Biological speciesSuid alphaherpesvirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.53 Å
AuthorsZheng Q / Li S / Zha Z / Sun H
Funding support1 items
OrganizationGrant numberCountry
Not funded
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

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Structure visualization

Supplemental images

emd_31612.png

Downloads & links

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Map

FileDownload / File: emd_31612.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-5.5994196 - 9.650452
Average (Standard dev.)-0.0039322046 (±0.86028945)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of PRV A-capsid

EntireName: Cryo-EM structure of PRV A-capsid
Components
  • Virus: Suid alphaherpesvirus 1
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Small capsomere-interacting protein

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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

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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

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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

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Macromolecule #3: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 10 / 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

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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

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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 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: 60.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8899

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