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- EMDB-57488: Cryo-electron tomogram of cryo-FIB milled yeast cells frozen in H... -

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Basic information

Entry
Database: EMDB / ID: EMD-57488
TitleCryo-electron tomogram of cryo-FIB milled yeast cells frozen in HPF Autogrid Planchettes
Map dataCryo-electron tomogram of cryo-FIB milled yeast cells
Sample
  • Cell: Cryo-FIB milled yeast cell
KeywordsIn-situ ribosome complexes / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsWeber MS / Weiss GL
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMSGI3_226208 Switzerland
CitationJournal: To Be Published
Title: A simplified High-Pressure Freezing Workflow in Autogrids
Authors: Weber MS / Epprecht T / Xu J / Weiss GL
History
DepositionApr 17, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57488.png

Downloads & links

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Map

FileDownload / File: emd_57488.map.gz / Format: CCP4 / Size: 351.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of cryo-FIB milled yeast cells
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
21.42 Å/pix.
x 250 pix.
= 5355. Å		21.42 Å/pix.
x 720 pix.
= 15422.4 Å		21.42 Å/pix.
x 512 pix.
= 10967.04 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: 21.42 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-23.865929000000001 - 8.281955999999999
Average (Standard dev.)-0.029728586 (±0.5495433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720512250
Spacing512720250
CellA: 10967.04 Å / B: 15422.4 Å / C: 5355.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-FIB milled yeast cell

EntireName: Cryo-FIB milled yeast cell
Components
  • Cell: Cryo-FIB milled yeast cell

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Supramolecule #1: Cryo-FIB milled yeast cell

SupramoleculeName: Cryo-FIB milled yeast cell / 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: 6.5 / Component - Concentration: 1.0 x / Component - Name: YPD medium
Details: 10 g/l yeast extract, 20 g/l peptone, 20 g/l glucose
VitrificationCryogen name: NITROGEN
High pressure freezingInstrument: OTHER
Details: High pressure freezing was performed on clipped EM-grids with the Waffle method, using an autogrid planchette system with a Waffle lid without a spacer. The planchettes were pre-coated with ...Details: High pressure freezing was performed on clipped EM-grids with the Waffle method, using an autogrid planchette system with a Waffle lid without a spacer. The planchettes were pre-coated with 0.5% cetyl palmitate in chloroform and a drop of 1-hexadecene was added to the autogrid planchette right before adding the grid.. The value given for _em_high_pressure_freezing.instrument is Leica EM-ICE. This is not in a list of allowed values {'LEICA EM PACT2', 'LEICA EM HPM100', 'OTHER', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'BAL-TEC HPM 010'} so OTHER is written into the XML file.
Cryo protectantNone
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 20000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: Cryo-Liftout using the SOLIST method was performed using a TFS Hydra instrument.. The value given for _em_focused_ion_beam.instrument is TFS Hydra. This is not in a list ...Focused ion beam - Details: Cryo-Liftout using the SOLIST method was performed using a TFS Hydra instrument.. The value given for _em_focused_ion_beam.instrument is TFS Hydra. 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
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 2.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 33000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD (ver. 5.1) / Number images used: 37
CTF correctionSoftware - Name: IMOD (ver. 5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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