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- EMDB-19550: cryoEM structure of purified Acs1 filament from meiotic yeast cells -

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Basic information

Entry
Database: EMDB / ID: EMD-19550
TitlecryoEM structure of purified Acs1 filament from meiotic yeast cells
Map data
Sample
  • Complex: Purified Acetyl-CoA synthetase 1 filament from meiotic yeast cells
    • Protein or peptide: Acetyl-CoA synthetase 1 from yeast SK1 strain
Keywordsmetabolic enzyme / filament / cryoEM / CYTOSOLIC PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae SK1 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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_19550.png

Downloads & links

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Map

FileDownload / File: emd_19550.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.5015126 - 2.7241554
Average (Standard dev.)0.00805274 (±0.10265896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19550_msk_1.map
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Half map: #1

Fileemd_19550_half_map_1.map
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Half map: #2

Fileemd_19550_half_map_2.map
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Sample components

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Entire : Purified Acetyl-CoA synthetase 1 filament from meiotic yeast cells

EntireName: Purified Acetyl-CoA synthetase 1 filament from meiotic yeast cells
Components
  • Complex: Purified Acetyl-CoA synthetase 1 filament from meiotic yeast cells
    • Protein or peptide: Acetyl-CoA synthetase 1 from yeast SK1 strain

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Supramolecule #1: Purified Acetyl-CoA synthetase 1 filament from meiotic yeast cells

SupramoleculeName: Purified Acetyl-CoA synthetase 1 filament from meiotic yeast cells
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: Acetyl-CoA synthetase 1 from yeast SK1 strain

MacromoleculeName: Acetyl-CoA synthetase 1 from yeast SK1 strain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae SK1 (yeast)
SequenceString: MSPSAVQSSK LEEQSSEID K LKAKMSQS AS TAQQKKE HEY EHLTSV KIVP QRPIS DRLQP AIAT HYSPHL DGL QDYQRLH KE SIEDPAKF F GSKATQFLN WSKPFDKVFI PDSKTGRPS F QNNAWFLN GQ LNACYNC VDR HALKTP NKKA IIFEG ...String:
MSPSAVQSSK LEEQSSEID K LKAKMSQS AS TAQQKKE HEY EHLTSV KIVP QRPIS DRLQP AIAT HYSPHL DGL QDYQRLH KE SIEDPAKF F GSKATQFLN WSKPFDKVFI PDSKTGRPS F QNNAWFLN GQ LNACYNC VDR HALKTP NKKA IIFEG DEPGQ GYSI TYKELL EEV CQVAQVL TY SMGVRKGD T VAVYMPMVP EAIITLLAIS RIGAIHSVV F AGFSSNSL RD RINDGDS KVV ITTDES NRGG KVIET KRIVD DALR ETPGVR HVL VYRKTNN PS VAFHAPRD L DWATEKKKY KTYYPCTPVD SEDPLFLLY T SGSTGAPK GV QHSTAGY LLG ALLTMR YTFD THQED VFFTA GDIG WITGHT YVV YGPLLYG CA TLVFEGTP A YPNYSRYWD IIDEHKVTQF YVAPTALRL L KRAGDSYI EN HSLKSLR CLG SVGEPI AAEV WEWYS EKIGK NEIP IVDTYW QTE SGSHLVT PL AGGVTPMK P GSASFPFFG IDAVVLDPNT GEELNTSHA E GVLAVKAA WP SFARTIW KNH DRYLDT YLNP YPGYY FTGDG AAKD KDGYIW ILG RVDDVVN VS GHRLSTAE I EAAIIEDPI VAECAVVGFN DDLTGQAVA A FVVLKNKS NW STATDDE LQD IKKHLV FTVR KDIGP FAAPK LIIL VDDLPK TRS GKIMRRI LR KILAGESD Q LGDVSTLSN PGIVRHLIDS VKL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: the initial model is determined from cryoEM structure of Acs1 determined by filamentID (D_1292136168)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 7310
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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