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- EMDB-17823: Tomogram of the Emiliania huxleyi virus 201 (EhV-201) purified pa... -

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Basic information

Entry
Database: EMDB / ID: EMD-17823
TitleTomogram of the Emiliania huxleyi virus 201 (EhV-201) purified particles used for subtomogram averaging.
Map dataOriginal tomogram
Sample
  • Virus: Emiliania huxleyi virus 201
Keywordscryo-EM / subtomogram averaging / EhV-201 / enveloped virus / capsid / major capsid protein / VIRUS
Biological speciesEmiliania huxleyi virus 201
Methodelectron tomography / cryo EM / Resolution: 25.0 Å
AuthorsHomola M / Buttner CR / Fuzik T / Novacek J / Chaillet M / Forster F / Plevka P
Funding support Czech Republic, European Union, 2 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
European Research Council (ERC)101043454European Union
CitationJournal: Sci Adv / Year: 2024
Title: Structure and replication cycle of a virus infecting climate-modulating alga .
Authors: Miroslav Homola / Carina R Büttner / Tibor Füzik / Pavel Křepelka / Radka Holbová / Jiří Nováček / Marten L Chaillet / Jakub Žák / Danyil Grybchuk / Friedrich Förster / William H ...Authors: Miroslav Homola / Carina R Büttner / Tibor Füzik / Pavel Křepelka / Radka Holbová / Jiří Nováček / Marten L Chaillet / Jakub Žák / Danyil Grybchuk / Friedrich Förster / William H Wilson / Declan C Schroeder / Pavel Plevka /
Abstract: The globally distributed marine alga has cooling effect on the Earth's climate. The population density of is restricted by viruses, including virus 201 (EhV-201). Despite the impact of viruses ...The globally distributed marine alga has cooling effect on the Earth's climate. The population density of is restricted by viruses, including virus 201 (EhV-201). Despite the impact of viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect by using fivefold vertices to bind to and fuse the virus' inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from cells, which enables the continuous release of virions by exocytosis.
History
DepositionJul 11, 2023-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17823.png

Downloads & links

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Map

FileDownload / File: emd_17823.map.gz / Format: CCP4 / Size: 739.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOriginal tomogram
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12.48 Å/pix.
x 296 pix.
= 3694.08 Å		12.48 Å/pix.
x 960 pix.
= 11980.8 Å		12.48 Å/pix.
x 682 pix.
= 8511.359 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 12.48 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-1.333431 - 3.3279037
Average (Standard dev.)0.000000000000628 (±0.05917935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960682296
Spacing682960296
CellA: 8511.359 Å / B: 11980.8 Å / C: 3694.0798 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Place back of virion vertices using coordinates from 3D refinement.

Fileemd_17823_additional_1.map
AnnotationPlace back of virion vertices using coordinates from 3D refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Emiliania huxleyi virus 201

EntireName: Emiliania huxleyi virus 201
Components
  • Virus: Emiliania huxleyi virus 201

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Supramolecule #1: Emiliania huxleyi virus 201

SupramoleculeName: Emiliania huxleyi virus 201 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: EhV-201 was propagated on a non-calcifying Emiliania huxleyi strain (CCPM 2090).
NCBI-ID: 181210 / Sci species name: Emiliania huxleyi virus 201 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Emiliania huxleyi CCMP1516 (eukaryote) / Strain: CCMP 2090
Virus shellShell ID: 1 / Name: inner membrane
Virus shellShell ID: 2 / Name: capsid / Diameter: 1990.0 Å / T number (triangulation number): 169
Virus shellShell ID: 3 / Name: outer membrane / Diameter: 2110.0 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Component - Name: sea salt
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 5e-05 kPa / Details: top side only
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV
Details: Sample: 3.5 ul; Wait time: 10 s; Blot time: 3 s; Blot force: -2; Drain time: 0 s.
DetailsThe viral sample was concentrated down to 1x10^10 plaque-forming units per ml (PFU ml^-1)
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 6 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4323 / Average exposure time: 1.5 sec. / Average electron dose: 2.42 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 2.0 µm / Calibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Number images used: 1

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