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- EMDB-10010: Atomic structure of the Epstein-Barr portal, structure I -

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Basic information

Entry
Database: EMDB / ID: EMD-10010
TitleAtomic structure of the Epstein-Barr portal, structure I
Map data
SampleDNA packaging viral protein:
Portal protein
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / DNA packaging / viral release from host cell / virion / host cell nucleus / Portal protein
Function and homology information
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus) / Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsMachon C / Fabrega-Ferrer M / Zhou D / Cuervo A / Carrascosa JL / Stuart DI / Coll M
Funding support Spain, 7 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessRYC-2011-09071 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBPF2014-53550-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU 2014-54181 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSEV-2013-0347 Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
European Commission653706
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 ReportPDB-ID: 6rvr

SummaryFull reportAbout validation report
History
DepositionMay 31, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateSep 18, 2019-
Current statusSep 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6rvr
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10010.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 220 pix.
= 242. Å
1.1 Å/pix.
x 220 pix.
= 242. Å
1.1 Å/pix.
x 220 pix.
= 242. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0229 / Movie #1: 0.0229
Minimum - Maximum-0.05884046 - 0.12890957
Average (Standard dev.)0.001016252 (±0.005942787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 242.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z242.000242.000242.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0590.1290.001

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Supplemental data

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Sample components

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Entire DNA packaging viral protein

EntireName: DNA packaging viral protein / Number of components: 2

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Component #1: protein, DNA packaging viral protein

ProteinName: DNA packaging viral protein / Recombinant expression: No
SourceSpecies: Human gammaherpesvirus 4 (Epstein-Barr virus)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Cell of expression system: Sf9 cell line

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Component #2: protein, Portal protein

ProteinName: Portal protein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 68.539641 kDa
SourceSpecies: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 44 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C12 (12 fold cyclic) / Number of projections: 73395
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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