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- EMDB-38295: SPACEtomo example tomograms of Baker's Yeast -

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Basic information

Entry
Database: EMDB / ID: EMD-38295
TitleSPACEtomo example tomograms of Baker's Yeast
Map dataSPACEtomo example tomogram showing a mitochondrium
Sample
  • Cell: Baker's Yeast
KeywordscryoET / tomogram / CYTOSOLIC PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsEisenstein F / Danev R
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02554 Japan
Japan Society for the Promotion of Science (JSPS)21F20764 Japan
CitationJournal: Biorxiv / Year: 2024
Title: Smart Parallel Automated Cryo Electron tomography
Authors: Eisenstein F / Fukuda Y / Danev R
History
DepositionDec 12, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38295.png

Downloads & links

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Map

FileDownload / File: emd_38295.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSPACEtomo example tomogram showing a mitochondrium
Voxel sizeX=Y=Z: 8.36 Å
Density
Minimum - Maximum-3.6620421 - 1.1905801
Average (Standard dev.)0.03319033 (±0.054632302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-72
Dimensions14401024300
Spacing10241440300
CellA: 8560.64 Å / B: 12038.399 Å / C: 2508.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: SPACEtomo example tomogram showing the nuclear envelope

Fileemd_38295_additional_1.map
AnnotationSPACEtomo example tomogram showing the nuclear envelope
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Baker's Yeast

EntireName: Baker's Yeast (brewer's yeast)
Components
  • Cell: Baker's Yeast

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Supramolecule #1: Baker's Yeast

SupramoleculeName: Baker's Yeast / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE-PROPANE
Cryo protectant15 % dextran and 2 % glucose
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 60 / Focused ion beam - Temperature: 78 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 8 / Average exposure time: 1.0 sec. / Average electron dose: 4.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 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 / Details: Tomogram was denoised using cryo-CARE / Number images used: 40

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