+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31611 | |||||||||
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Title | Cryo-EM structure of pseudorabies virus C-capsid | |||||||||
Map data | ||||||||||
Sample |
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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 / host cell / 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 | |||||||||
Biological species | Suid alphaherpesvirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.43 Å | |||||||||
Authors | Zheng Q / Li S / Zha Z / Sun H | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31611.map.gz | 7.2 GB | EMDB map data format | |
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Header (meta data) | emd-31611-v30.xml emd-31611.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_31611.png | 54.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31611 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31611 | HTTPS FTP |
-Validation report
Summary document | emd_31611_validation.pdf.gz | 715.2 KB | Display | EMDB validaton report |
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Full document | emd_31611_full_validation.pdf.gz | 714.8 KB | Display | |
Data in XML | emd_31611_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_31611_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31611 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31611 | HTTPS FTP |
-Related structure data
Related structure data | 7fj1MC 7fj3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31611.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.117 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Suid alphaherpesvirus 1
Entire | Name: Suid alphaherpesvirus 1 |
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Components |
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-Supramolecule #1: Suid alphaherpesvirus 1
Supramolecule | Name: 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
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: Suid alphaherpesvirus 1 |
Molecular weight | Theoretical: 146.101984 KDa |
Sequence | String: 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
Macromolecule | Name: Triplex capsid protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Suid alphaherpesvirus 1 |
Molecular weight | Theoretical: 31.763766 KDa |
Sequence | String: 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
Macromolecule | Name: Capsid vertex component 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Suid alphaherpesvirus 1 |
Molecular weight | Theoretical: 64.304371 KDa |
Sequence | String: 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
Macromolecule | Name: Small capsomere-interacting protein / type: protein_or_peptide / ID: 4 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: Suid alphaherpesvirus 1 |
Molecular weight | Theoretical: 11.509209 KDa |
Sequence | String: MSFDPNNPRT ITAQTLEGAL PVDILLRLNR ATGLQMDAAE AHAIVEDARR TLFIGTSLAL VNLRRAHDKH LVERQPMFAT SDYSSWARP TVGLKRTFCP RPPP |
-Macromolecule #5: Triplex capsid protein 1
Macromolecule | Name: Triplex capsid protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Suid alphaherpesvirus 1 |
Molecular weight | Theoretical: 40.008594 KDa |
Sequence | String: 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
Macromolecule | Name: DNA packaging tegument protein UL25 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Suid alphaherpesvirus 1 |
Molecular weight | Theoretical: 57.412797 KDa |
Sequence | String: 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
Macromolecule | Name: VP1/2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Suid alphaherpesvirus 1 |
Molecular weight | Theoretical: 7.069434 KDa |
Sequence | String: RVVESDTLIN RRYMRATGLG ALALLIAACR LIARRLRETR TTLKGSARRF NVDLFQVRLI LG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14252 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |