+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30155 | ||||||||||||||||||
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Title | Epstein-Barr virus, C12 portal dodecamer | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | Epstein-Barr virus / portal dodecomer / tegumented capsid / VIRAL PROTEIN | ||||||||||||||||||
Function / homology | Herpesvirus portal protein / Herpesvirus UL6 like / chromosome organization => GO:0051276 / virion component => GO:0044423 / viral release from host cell / host cell nucleus / Portal protein Function and homology information | ||||||||||||||||||
Biological species | Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) / Human gammaherpesvirus 4 (Epstein-Barr virus) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||||||||
Authors | Li Z / Yu X / Zeng M | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: Cell Res / Year: 2020 Title: CryoEM structure of the tegumented capsid of Epstein-Barr virus. Authors: Zhihai Li / Xiao Zhang / Lili Dong / Jingjing Pang / Miao Xu / Qian Zhong / Mu-Sheng Zeng / Xuekui Yu / Abstract: Epstein-Barr virus (EBV) is the primary cause of infectious mononucleosis and has been shown to be closely associated with various malignancies. Here, we present a complete atomic model of EBV, ...Epstein-Barr virus (EBV) is the primary cause of infectious mononucleosis and has been shown to be closely associated with various malignancies. Here, we present a complete atomic model of EBV, including the icosahedral capsid, the dodecameric portal and the capsid-associated tegument complex (CATC). Our in situ portal from the tegumented capsid adopts a closed conformation with its channel valve holding the terminal viral DNA and with its crown region firmly engaged by three layers of ring-like dsDNA, which, together with the penton flexibility, effectively alleviates the capsid inner pressure placed on the portal cap. In contrast, the CATCs, through binding to the flexible penton vertices in a stoichiometric manner, accurately increase the inner capsid pressure to facilitate the pressure-driven genome delivery. Together, our results provide important insights into the mechanism by which the EBV capsid, portal, packaged genome and the CATCs coordinately achieve a pressure balance to simultaneously benefit both viral genome retention and ejection. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30155.map.gz | 16.7 MB | EMDB map data format | |
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Header (meta data) | emd-30155-v30.xml emd-30155.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_30155.png | 112.3 KB | ||
Filedesc metadata | emd-30155.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30155 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30155 | HTTPS FTP |
-Validation report
Summary document | emd_30155_validation.pdf.gz | 594.9 KB | Display | EMDB validaton report |
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Full document | emd_30155_full_validation.pdf.gz | 594.4 KB | Display | |
Data in XML | emd_30155_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | emd_30155_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30155 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30155 | HTTPS FTP |
-Related structure data
Related structure data | 7bqtMC 7bqxC 7br7C 7br8C 7bsiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30155.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human gammaherpesvirus 4
Entire | Name: Human gammaherpesvirus 4 (Epstein-Barr virus) |
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Components |
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-Supramolecule #1: Human gammaherpesvirus 4
Supramolecule | Name: Human gammaherpesvirus 4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10376 / Sci species name: Human gammaherpesvirus 4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: B95-8 |
Molecular weight | Theoretical: 68.539641 KDa |
Sequence | String: MFNMNVDESA SGALGSSAIP VHPTPASVRL FEILQGKYAY VQGQTIYANL RNPGVFSRQV FTHLFKRAIS HCTYDDVLHD WNKFEACIQ KRWPSDDSCA SRFRESTFES WSTTMKLTVR DLLTTNIYRV LHSRSVLSYE RYVDWICATG MVPAVKKPIT Q ELHSKIKS ...String: MFNMNVDESA SGALGSSAIP VHPTPASVRL FEILQGKYAY VQGQTIYANL RNPGVFSRQV FTHLFKRAIS HCTYDDVLHD WNKFEACIQ KRWPSDDSCA SRFRESTFES WSTTMKLTVR DLLTTNIYRV LHSRSVLSYE RYVDWICATG MVPAVKKPIT Q ELHSKIKS LRDRCVCREL GHERTIRSIG TELYEATKEI IESLNSTFIP QFTEVTIEYL PRSDEYVAYY CGRRIRLHVL FP PAIFAGT VTFDSPVQRL YQNIFMCYRT LEHAKICQLL NTAPLKAIVG HGGRDMYKDI LAHLEQNSQR KDPKKELLNL LVK LSENKT ISGVTDVVEE FITDASNNLV DRNRLFGQPG ETAAQGLKKK VSNTVVKCLT DQINEQFDQI NGLEKERELY LKKI RSMES QLQASLGPGG NNPAASAPAA VAAEAASVDI LTGSTASAIE KLFNSPSASL GARVSGHNES ILNSFVSQYI PPSRE MTKD LTELWESELF NTFKLTPVVD NQGQRLYVRY SSDTISILLG PFTYLVAELS PVELVTDVYA TLGIVEIIDE LYRSSR LAI YIEDLGRKYC PASATGGDHG IRQAPSARGD TEPDHAKSKP ARDPPPGAGS UniProtKB: Portal protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #0 - Average electron dose: 48.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #1 - Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |