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- PDB-7br8: Epstein-Barr virus, C5 penton vertex, CATC absent. -

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Basic information

Entry
Database: PDB / ID: 7br8
TitleEpstein-Barr virus, C5 penton vertex, CATC absent.
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRAL PROTEIN / C5 penton vertex / CATC absent / tegumented capsid
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
Gammaherpesvirus capsid / Gammaherpesvirus capsid protein / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Triplex capsid protein 1 / Major capsid protein / Small capsomere-interacting protein / Triplex capsid protein 2
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi, Z. / Yu, X.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
National Natural Science Foundation of China (NSFC)81830090 China
National Natural Science Foundation of China (NSFC)81702001 China
Ministry of Science and Technology (MoST, China)2017YFA0505600 China
Ministry of Science and Technology (MoST, China)2016YFA0502101 China
CitationJournal: 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
DepositionMar 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
m: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
2: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
W: Major capsid protein
x: Major capsid protein
y: Small capsomere-interacting protein
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
l: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)1,074,35916
Polymers1,074,35916
Non-polymers00
Water00
1
m: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
2: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
W: Major capsid protein
x: Major capsid protein
y: Small capsomere-interacting protein
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
l: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
x 5


Theoretical massNumber of molelcules
Total (without water)5,371,79480
Polymers5,371,79480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
Buried area103620 Å2
ΔGint-574 kcal/mol
Surface area306170 Å2
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C5 (5 fold cyclic))

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Components

#1: Protein
Small capsomere-interacting protein


Mass: 18169.100 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P14348
#2: Protein
Major capsid protein / MCP


Mass: 154086.828 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P03226
#3: Protein Triplex capsid protein 1


Mass: 39231.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P03187
#4: Protein
Triplex capsid protein 2


Mass: 33654.039 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P25214
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human gammaherpesvirus 4 / Type: VIRUS / Source: NATURAL
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2RELION3image acquisition
4RELION3CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137356 / Symmetry type: POINT

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