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- EMDB-19554: cryo-tomogram of FIB-milled meiotic yeast cell containing filamen... -

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Basic information

Entry
Database: EMDB / ID: EMD-19554
Titlecryo-tomogram of FIB-milled meiotic yeast cell containing filaments in the nucleus
Map data
Sample
  • Cell: cryo FIB-milled meiotic yeast cells
Keywordsmetabolic enzyme / filament / cryoET / CYTOSOLIC PROTEIN / nucleus
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsHugener J / Xu J / Wettstein R / Ioannidi L / Velikov D / Wollweber F / Henggeler A / Matos J / Pilhofer M
Funding support Switzerland, European Union, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation176108 Switzerland
European Research Council (ERC)101002629European Union
CitationJournal: Cell(Cambridge,Mass.) / Year: 2024
Title: FilamentID reveals the composition and function of metabolic enzyme polymers during gametogenesis
Authors: Hugener J / Xu J / Wettstein R / Ioannidi L / Velikov D / Wollweber F / Henggeler A / Matos J / Pilhofer M
History
DepositionFeb 5, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19554.png

Downloads & links

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Map

FileDownload / File: emd_19554.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
17.36 Å/pix.
x 315 pix.
= 5468.4 Å		17.36 Å/pix.
x 928 pix.
= 16110.08 Å		17.36 Å/pix.
x 960 pix.
= 16665.602 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: 17.36 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-219.000499999999988 - 246.772420000000011
Average (Standard dev.)0.000000000719867 (±29.140308000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928960315
Spacing960928315
CellA: 16665.602 Å / B: 16110.08 Å / C: 5468.4004 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 meiotic yeast cells

EntireName: cryo FIB-milled meiotic yeast cells
Components
  • Cell: cryo FIB-milled meiotic yeast cells

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Supramolecule #1: cryo FIB-milled meiotic yeast cells

SupramoleculeName: cryo FIB-milled meiotic yeast cells / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: SK1

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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: 7
VitrificationCryogen name: ETHANE-PROPANE
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: 1500 / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 4000 / Focused ion beam - Final thickness: 300
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam 550. 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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