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- EMDB-19555: cryo-tomogram of FIB-milled meiotic yeast cell containing filamen... -

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Basic information

Entry
Database: EMDB / ID: EMD-19555
Titlecryo-tomogram of FIB-milled meiotic yeast cell containing filaments in the cytoplasm
Map data
Sample
  • Cell: cryo FIB-milled meiotic yeast cells
Keywordsmetabolic enzyme / filament / cryoET / CYTOSOLIC PROTEIN / cytoplasm
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 / Year: 2024
Title: FilamentID reveals the composition and function of metabolic enzyme polymers during gametogenesis.
Authors: Jannik Hugener / Jingwei Xu / Rahel Wettstein / Lydia Ioannidi / Daniel Velikov / Florian Wollweber / Adrian Henggeler / Joao Matos / Martin Pilhofer /
Abstract: Gamete formation and subsequent offspring development often involve extended phases of suspended cellular development or even dormancy. How cells adapt to recover and resume growth remains poorly ...Gamete formation and subsequent offspring development often involve extended phases of suspended cellular development or even dormancy. How cells adapt to recover and resume growth remains poorly understood. Here, we visualized budding yeast cells undergoing meiosis by cryo-electron tomography (cryoET) and discovered elaborate filamentous assemblies decorating the nucleus, cytoplasm, and mitochondria. To determine filament composition, we developed a "filament identification" (FilamentID) workflow that combines multiscale cryoET/cryo-electron microscopy (cryoEM) analyses of partially lysed cells or organelles. FilamentID identified the mitochondrial filaments as being composed of the conserved aldehyde dehydrogenase Ald4 and the nucleoplasmic/cytoplasmic filaments as consisting of acetyl-coenzyme A (CoA) synthetase Acs1. Structural characterization further revealed the mechanism underlying polymerization and enabled us to genetically perturb filament formation. Acs1 polymerization facilitates the recovery of chronologically aged spores and, more generally, the cell cycle re-entry of starved cells. FilamentID is broadly applicable to characterize filaments of unknown identity in diverse cellular contexts.
History
DepositionFeb 5, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19555.png

Downloads & links

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Map

FileDownload / File: emd_19555.map.gz / Format: CCP4 / Size: 706.9 MB / 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 208 pix.
= 3610.88 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-244.609440000000006 - 264.689450000000022
Average (Standard dev.)-0.000000000723376 (±20.259170000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928960208
Spacing960928208
CellA: 16665.602 Å / B: 16110.08 Å / C: 3610.8801 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: 150
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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