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Open data
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Basic information
Entry | Database: PDB / ID: 7bqt | ||||||||||||||||||
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Title | Epstein-Barr virus, C12 portal dodecamer | ||||||||||||||||||
![]() | Portal protein | ||||||||||||||||||
![]() | VIRAL PROTEIN / Epstein-Barr virus / portal dodecomer / tegumented capsid | ||||||||||||||||||
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![]() | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||||||||
![]() | Li, Z. / Yu, X. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 856.9 KB | Display | ![]() |
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PDB format | ![]() | 711.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30155MC ![]() 7bqxC ![]() 7br7C ![]() 7br8C ![]() 7bsiC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 68539.641 Da / Num. of mol.: 12 / Source method: isolated from a natural source Source: (natural) ![]() Strain: B95-8 / References: UniProt: P03213 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human gammaherpesvirus 4 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||
Electron gun | Electron source: ![]() | ||||||||||||
Electron lens | Mode: OTHER | ||||||||||||
Image recording |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22782 / Symmetry type: POINT |