[English] 日本語
Yorodumi
- EMDB-52589: Cryo-tomogram of FIB-milled wild-type untreated yeast cell -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52589
TitleCryo-tomogram of FIB-milled wild-type untreated yeast cell
Map data
Sample
  • Cell: Plunge-frozen, cryoFIB-milled WT 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

-
Structure visualization

Supplemental images

emd_52589.png

Downloads & links

-
Map

FileDownload / File: emd_52589.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-155.218610000000012 - 154.102429999999998
Average (Standard dev.)2.0331283 (±24.127393999999999)
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 °

-
Supplemental data

-
Sample components

-
Entire : Plunge-frozen, cryoFIB-milled WT yeast cell

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

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

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
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.

-
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

-
Image processing

Final reconstructionNumber images used: 41
CTF correctionType: NONE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more