+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30146 | ||||||||||||||||||
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Title | Epstein-Barr Virus, C1 tegumented capsid reconstruction | ||||||||||||||||||
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Sample |
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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 | ||||||||||||||||||
Biological species | Human gammaherpesvirus 4 (Epstein-Barr virus) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||||||||
Authors | Li Z / Zhang X / Zeng M / Yu X | ||||||||||||||||||
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_30146.map.gz | 911.8 MB | EMDB map data format | |
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Header (meta data) | emd-30146-v30.xml emd-30146.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | emd_30146.png | 203.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30146 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30146 | HTTPS FTP |
-Validation report
Summary document | emd_30146_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_30146_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_30146_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30146 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30146 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30146.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.62 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 / 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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-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 | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / 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 |