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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: Nat Methods / Year: 2024
Title: Smart parallel automated cryo-electron tomography.
Authors: Fabian Eisenstein / Yoshiyuki Fukuda / Radostin Danev /
Abstract: In situ cryo-electron tomography enables investigation of macromolecules in their native cellular environment. Samples have become more readily available owing to recent software and hardware ...In situ cryo-electron tomography enables investigation of macromolecules in their native cellular environment. Samples have become more readily available owing to recent software and hardware advancements. Data collection, however, still requires an experienced operator and appreciable microscope time to carefully select targets for high-throughput tilt series acquisition. Here, we developed smart parallel automated cryo-electron tomography (SPACEtomo), a workflow using machine learning approaches to fully automate the entire cryo-electron tomography process, including lamella detection, biological feature segmentation, target selection and parallel tilt series acquisition, all without the need for human intervention. This degree of automation will be essential for obtaining statistically relevant datasets and high-resolution structures of macromolecules in their native context.
History
DepositionDec 12, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.36 Å/pix.
x 300 pix.
= 2508. Å		8.36 Å/pix.
x 1440 pix.
= 12038.399 Å		8.36 Å/pix.
x 1024 pix.
= 8560.64 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: 8.36 Å
Density

Histogram

Histogram (log scale)
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 {'OTHER', 'DB235'} 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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