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- EMDB-19552: cryo sub-tomogram average of Ald4 filaments from purified meiotic... -

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Basic information

Entry
Database: EMDB / ID: EMD-19552
Titlecryo sub-tomogram average of Ald4 filaments from purified meiotic yeast mitochondria
Map data
Sample
  • Complex: Ald4 polymer from purified meiotic yeast mitochondria
    • Protein or peptide: Aldehyde dehydrogenase 4
Keywordsmetabolic enzyme / filament / cryoET / mitochondria / CYTOSOLIC PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae SK1 (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 44.0 Å
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_19552.png

Downloads & links

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Map

FileDownload / File: emd_19552.map.gz / Format: CCP4 / Size: 128.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
11 Å/pix.
x 32 pix.
= 352. Å		11 Å/pix.
x 32 pix.
= 352. Å		11 Å/pix.
x 32 pix.
= 352. Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-4.478755 - 5.698921
Average (Standard dev.)-0.0229154 (±1.1953875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions323232
Spacing323232
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19552_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_19552_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Ald4 polymer from purified meiotic yeast mitochondria

EntireName: Ald4 polymer from purified meiotic yeast mitochondria
Components
  • Complex: Ald4 polymer from purified meiotic yeast mitochondria
    • Protein or peptide: Aldehyde dehydrogenase 4

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Supramolecule #1: Ald4 polymer from purified meiotic yeast mitochondria

SupramoleculeName: Ald4 polymer from purified meiotic yeast mitochondria / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: SK1

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Macromolecule #1: Aldehyde dehydrogenase 4

MacromoleculeName: Aldehyde dehydrogenase 4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae SK1 (yeast)
SequenceString: MFSRSTLCLK TSASSIGRL Q LRYFSHLP MT VPIKLPN GLE YEQPTG LFIN NKFVP SKQNK TFEV INPSTE EEI CHIYEGR ED DVEEAVQA A DRAFSNGSW NGIDPIDRGK ALYRLAELI E QDKDVIAS IE TLDNGKA ISS SRGDVD LVIN YLKSS ...String:
MFSRSTLCLK TSASSIGRL Q LRYFSHLP MT VPIKLPN GLE YEQPTG LFIN NKFVP SKQNK TFEV INPSTE EEI CHIYEGR ED DVEEAVQA A DRAFSNGSW NGIDPIDRGK ALYRLAELI E QDKDVIAS IE TLDNGKA ISS SRGDVD LVIN YLKSS AGFAD KIDG RMIDTG RTH FSYTKRQ PL GVCGQIIP W NFPLLMWAW KIAPALVTGN TVVLKTAES T PLSALYVS KY IPQAGIP PGV INIVSG FGKI VGEAI TNHPK IKKV AFTGST ATG RHIYQSA AA GLKKVTLE L GGKSPNIVF ADAELKKAVQ NIILGIYYN S GEVCCAGS RV YVEESIY DKF IEEFKA ASES IKVGD PFDES TFQG AQTSQM QLN KILKYVD IG KNEGATLI T GGERLGSKG YFIKPTVFGD VKEDMRIVK E EIFGPVVT VT KFKSADE VIN MANDSE YGLA AGIHT SNINT ALKV ADRVNA GTV WINTYND FH HAVPFGGF N ASGLGREMS VDALQNYLQV KAVRAKLDE

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE-PROPANE

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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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 44.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 564
ExtractionNumber tomograms: 3 / Number images used: 564
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION

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