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- EMDB-52590: Cryo-tomogram of a FIB-milled stm1-deletion untreated yeast cell -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-52590
TitleCryo-tomogram of a FIB-milled stm1-deletion untreated yeast cell
Map data
Sample
  • Cell: Plunge-frozen, cryoFIB-milled stm1-deletion yeast cell
KeywordsYeast / cytoplasm / ribosome
Biological speciesS.cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsBonassera M / Peter M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030-200426 Switzerland
CitationJournal: Mol Cell / Year: 2025
Title: Stm1 regulates Ifh1 activity revealing crosstalk between ribosome biogenesis and ribosome dormancy.
Authors: Eliana Bianco / Martina Bonassera / Federico Uliana / Janny Tilma / Martin Winkler / Sevil Zencir / Alvar Gossert / Michaela Oborská-Oplová / Reinhard Dechant / Jannik Hugener / Vikram ...Authors: Eliana Bianco / Martina Bonassera / Federico Uliana / Janny Tilma / Martin Winkler / Sevil Zencir / Alvar Gossert / Michaela Oborská-Oplová / Reinhard Dechant / Jannik Hugener / Vikram Govind Panse / Martin Pilhofer / Benjamin Albert / Philipp Kimmig / Matthias Peter /
Abstract: Nutrient abundance boosts ribosome biogenesis, whereas ribosome dormancy factors limit ribosome degradation upon starvation. The equilibrium between the two pathways governs cell growth. In this ...Nutrient abundance boosts ribosome biogenesis, whereas ribosome dormancy factors limit ribosome degradation upon starvation. The equilibrium between the two pathways governs cell growth. In this study, we identified suppressor of Tom1 (Stm1) as a molecular link between ribosome protection and biogenesis in Saccharomyces cerevisiae. While Stm1 was previously described as a dormancy factor, we show that it activates Ifh1, a transcriptional activator of ribosomal protein genes. Stm1 transiently localizes to the nucleolus, where it interacts with pre-ribosomes and directly binds RNA and Ifh1 through its C-terminal intrinsically disordered region (IDR). Although the IDR is dispensable for ribosome protection, its loss compromises cell growth. The IDR is phosphorylated upon nutrient starvation, which disrupts its interaction with Ifh1. Our findings reveal a molecular pathway sensing and adjusting ribosome abundance in response to nutrient availability, reinforcing the relevance of regulated ribosome homeostasis in physiology and disease.
History
DepositionJan 22, 2025-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52590.png

Downloads & links

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Map

FileDownload / File: emd_52590.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 400 pix.
= 1072. Å		2.68 Å/pix.
x 1440 pix.
= 3859.2 Å		2.68 Å/pix.
x 1024 pix.
= 2744.32 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: 2.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-215.227159999999998 - 165.864229999999992
Average (Standard dev.)2.1718414 (±23.53321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-833831-799
Dimensions14401024400
Spacing10241440400
CellA: 2744.32 Å / B: 3859.2002 Å / C: 1072.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Plunge-frozen, cryoFIB-milled stm1-deletion yeast cell

EntireName: Plunge-frozen, cryoFIB-milled stm1-deletion yeast cell
Components
  • Cell: Plunge-frozen, cryoFIB-milled stm1-deletion yeast cell

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Supramolecule #1: Plunge-frozen, cryoFIB-milled stm1-deletion yeast cell

SupramoleculeName: Plunge-frozen, cryoFIB-milled stm1-deletion yeast cell
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: S.cerevisiae (brewer's yeast)

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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: 6.8
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: 1000 / Focused ion beam - Final thickness: 200
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 {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 145.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 8.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41
CTF correctionType: NONE

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