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- EMDB-19556: cryo-tomogram of purified meiotic yeast mitochondrion containing ... -

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Basic information

Entry
Database: EMDB / ID: EMD-19556
Titlecryo-tomogram of purified meiotic yeast mitochondrion containing Ald4 filaments
Map data
Sample
  • Organelle or cellular component: purified mitochondria from meiotic yeast cells
Keywordsmetabolic enzyme / filament / cryoET / CYTOSOLIC PROTEIN / mitochondria
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_19556.png

Downloads & links

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Map

FileDownload / File: emd_19556.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11 Å/pix.
x 433 pix.
= 4763. Å		11 Å/pix.
x 928 pix.
= 10208. Å		11 Å/pix.
x 960 pix.
= 10560. 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: 11 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-194.323720000000009 - 298.00830000000002
Average (Standard dev.)-0.000000000855589 (±22.260470000000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928960433
Spacing960928433
CellA: 10560.0 Å / B: 10208.0 Å / C: 4763.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : purified mitochondria from meiotic yeast cells

EntireName: purified mitochondria from meiotic yeast cells
Components
  • Organelle or cellular component: purified mitochondria from meiotic yeast cells

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Supramolecule #1: purified mitochondria from meiotic yeast cells

SupramoleculeName: purified mitochondria from meiotic yeast cells / type: organelle_or_cellular_component / 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: 7.2
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.62 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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