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- PDB-7bsi: Epstein-Barr virus, one asymmetric unit structure of the icosahed... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bsi | ||||||||||||||||||
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Title | Epstein-Barr virus, one asymmetric unit structure of the icosahedral tegumented capsid | ||||||||||||||||||
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Function / homology | ![]() T=16 icosahedral viral capsid / ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | 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 | ![]() | 4.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30162MC ![]() 7bqtC ![]() 7bqxC ![]() 7br7C ![]() 7br8C 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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1 | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol![]() ![]() |
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Components
#1: Protein | Mass: 18169.100 Da / Num. of mol.: 16 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: B95-8 / References: UniProt: P14348 #2: Protein | Mass: 154086.828 Da / Num. of mol.: 16 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: B95-8 / References: UniProt: P03226 #3: Protein | Mass: 39231.539 Da / Num. of mol.: 5 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: B95-8 / References: UniProt: P03187 #4: Protein | Mass: 33654.039 Da / Num. of mol.: 10 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: B95-8 / References: UniProt: P25214 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Human gammaherpesvirus 4![]() |
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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![]() ![]() |
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 | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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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 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() ![]() | ||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32721 / Symmetry type: POINT |