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- PDB-6rvr: Atomic structure of the Epstein-Barr portal, structure I -

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Database: PDB / ID: 6rvr
TitleAtomic structure of the Epstein-Barr portal, structure I
ComponentsPortal protein
KeywordsVIRAL PROTEIN / DNA packaging
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / DNA packaging / viral release from host cell / virion / host cell nucleus / Portal protein / Portal protein
Function and homology information
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsMachon, C. / Fabrega-Ferrer, M. / Zhou, D. / Cuervo, A. / Carrascosa, J.L. / Stuart, D.I. / Coll, M.
Funding support Spain, 7items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessRYC-2011-09071 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU 2014-54181 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBPF2014-53550-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSEV-2013-0347 Spain
European Commission653706
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
CitationJournal: Nat Commun / Year: 2019
Title: Atomic structure of the Epstein-Barr virus portal.
Authors: Cristina Machón / Montserrat Fàbrega-Ferrer / Daming Zhou / Ana Cuervo / José L Carrascosa / David I Stuart / Miquel Coll /
Abstract: Herpesviridae is a vast family of enveloped DNA viruses that includes eight distinct human pathogens, responsible for diseases that range from almost asymptomatic to severe and life-threatening. ...Herpesviridae is a vast family of enveloped DNA viruses that includes eight distinct human pathogens, responsible for diseases that range from almost asymptomatic to severe and life-threatening. Epstein-Barr virus infects B-cells and epithelial cells, causing infectious mononucleosis, as well as a number of cancers. Epstein-Barr infection cannot be cured since neither vaccine nor antiviral drug treatments are available. All herpesviruses contain a linear double-stranded DNA genome, enclosed within an icosahedral capsid. Viral portal protein plays a key role in the procapsid assembly and DNA packaging. The portal is the entrance and exit pore for the viral genome, making it an attractive pharmacological target for the development of new antivirals. Here we present the atomic structure of the portal protein of Epstein-Barr virus, solved by cryo-electron microscopy at 3.5 Å resolution. The detailed architecture of this protein suggests that it plays a functional role in DNA retention during packaging.
Validation Report
SummaryFull reportAbout validation report
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release

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Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein

Theoretical massNumber of molelcules
Total (without water)822,47612

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area84060 Å2
ΔGint-507 kcal/mol
Surface area215820 Å2


#1: Protein
Portal protein

Mass: 68539.641 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1 / Gene: BBRF1 / Cell line (production host): Sf9 cell line / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0B6VPI0, UniProt: Q3KSR9*PLUS

Experimental details


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

Sample preparation

ComponentName: DNA packaging viral protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 cell line
Buffer solutionpH: 8
Buffer component
150 mMTris-HClTris1
220 mM2-mercaptoethanol1
3500 mMNaClSodium chloride1
41 mMEDTAEthylenediaminetetraacetic acid1
50.05 % w/vn-Dodecyl-B-D-Maltoside1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)


SoftwareName: PHENIX / Version: (dev_3584: phenix.real_space_refine) / Classification: refinement
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73395 / Symmetry type: POINT

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