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- EMDB-0189: Echovirus 30 Open particle without one pentamer -

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Basic information

Entry
Database: EMDB / Id: 189
TitleEchovirus 30 Open particle without one pentamer
Map dataEchovirus 30 Open particle without one pentamer
SampleEchovirus E30:
virus
SourceEchovirus E30
Methodsingle particle reconstruction / cryo EM / Resolution: 19.4 Å
AuthorsMukhamedova L / Buchta D / Fuzik T / Hrebik D / Levdansky Y / Moravcova J / Plevka P
CitationJournal: Nat Commun / Year: 2019
Title: Enterovirus particles expel capsid pentamers to enable genome release.
P-authors: David Buchta / Tibor Füzik / Dominik Hrebík / Yevgen Levdansky / Lukáš Sukeník / Liya Mukhamedova / Jana Moravcová / Robert Vácha / Pavel Plevka /
Abstract: Viruses from the genus Enterovirus are important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles to an activated state that is required for ...Viruses from the genus Enterovirus are important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles to an activated state that is required for genome release. However, the mechanism of enterovirus uncoating is not well understood. Here, we use cryo-electron microscopy to visualize virions of human echovirus 18 in the process of genome release. We discover that the exit of the RNA from the particle of echovirus 18 results in a loss of one, two, or three adjacent capsid-protein pentamers. The opening in the capsid, which is more than 120 Å in diameter, enables the release of the genome without the need to unwind its putative double-stranded RNA segments. We also detect capsids lacking pentamers during genome release from echovirus 30. Thus, our findings uncover a mechanism of enterovirus genome release that could become target for antiviral drugs.
DateDeposition: Aug 10, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Mar 20, 2019 / Last update: Mar 20, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_0189.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.06 Å/pix.
= 544.256 Å
512 pix
1.06 Å/pix.
= 544.256 Å
512 pix
1.06 Å/pix.
= 544.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density
Contour Level:0.018 (by author), 0.018 (movie #1):
Minimum - Maximum-0.009840471 - 0.045059573
Average (Standard dev.)0.0012383678 (0.005572821)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 544.256 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z544.256544.256544.256
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0100.0450.001

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Supplemental data

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Sample components

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Entire Echovirus E30

EntireName: Echovirus E30 / Number of components: 1

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Component #1: virus, Echovirus E30

VirusName: Echovirus E30 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Echovirus E30 / Strain: Bastianni
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Capsid / Diameter: 340.0 Å / T number(triangulation number): 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / Ph: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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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: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal), 79725.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1283 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C5 (5 fold cyclic) / Number of projections: 235
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 19.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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