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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: To Be Published
Title: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi
Authors: Homola M / Buttner CR / Fuzik T / Novacek J / Chaillet M / Forster F / Plevka P
History
DepositionJul 11, 2023-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing 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
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 77.0 K
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
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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