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- EMDB-51002: Untethered Cytoplasmic Fission Yeast Ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-51002
TitleUntethered Cytoplasmic Fission Yeast Ribosome
Map dataUntethered Cytosolic Ribosome of S. pombe generated by M
Sample
  • Complex: Cytoplasmic Ribosome Untethered to the Outer Mitochondrial Membrane
KeywordsHibernating / Yeast / In Situ / RACK1 / cytosolic / RIBOSOME / untethered
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 14.64 Å
AuthorsRosa H / Gemin O / Gluc M / Mattei S / Jomaa A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Ribosomes hibernate on mitochondria during cellular stress.
Authors: Olivier Gemin / Maciej Gluc / Higor Rosa / Michael Purdy / Moritz Niemann / Yelena Peskova / Simone Mattei / Ahmad Jomaa /
Abstract: Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated ...Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence.
History
DepositionJul 12, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51002.png

Downloads & links

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Map

FileDownload / File: emd_51002.map.gz / Format: CCP4 / Size: 13.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUntethered Cytosolic Ribosome of S. pombe generated by M
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.15 Å/pix.
x 154 pix.
= 639.1 Å		4.15 Å/pix.
x 154 pix.
= 639.1 Å		4.15 Å/pix.
x 154 pix.
= 639.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.003990194 - 0.020765621
Average (Standard dev.)0.00009993421 (±0.0016378692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions154154154
Spacing154154154
CellA=B=C: 639.10004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Untethered Cytosolic Ribosome of S. pombe Half-Map 2 generated by M

Fileemd_51002_half_map_1.map
AnnotationUntethered Cytosolic Ribosome of S. pombe Half-Map 2 generated by M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Untethered Cytosolic Ribosome of S. pombe Half-Map 1 generated by M

Fileemd_51002_half_map_2.map
AnnotationUntethered Cytosolic Ribosome of S. pombe Half-Map 1 generated by M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cytoplasmic Ribosome Untethered to the Outer Mitochondrial Membrane

EntireName: Cytoplasmic Ribosome Untethered to the Outer Mitochondrial Membrane
Components
  • Complex: Cytoplasmic Ribosome Untethered to the Outer Mitochondrial Membrane

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Supramolecule #1: Cytoplasmic Ribosome Untethered to the Outer Mitochondrial Membrane

SupramoleculeName: Cytoplasmic Ribosome Untethered to the Outer Mitochondrial Membrane
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 5.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.23 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 14.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.09) / Number subtomograms used: 12048
ExtractionNumber tomograms: 53 / Number images used: 12048
Final 3D classificationNumber classes: 1 / Avg.num./class: 12048
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion (Refine) + M (PPoses)
FSC plot (resolution estimation)

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