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- EMDB-54353: In situ Outer Mitochondrial Membrane Tethered Hibernating Ribosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-54353
TitleIn situ Outer Mitochondrial Membrane Tethered Hibernating Ribosomes from S. pombe under glucose depletion
Map dataFiltered Sharpened map generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose starvation (subset Tethered to the Outer mitochondrial membrane)
Sample
  • Complex: In situ Hibernating Ribosomes from Schizosaccharomyces pombe cultured under 7-day glucose depletion conditions
KeywordsHibernating / Yeast / In Situ / SNOR / RIBOSOME / pombe / glucose
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 6.0 Å
AuthorsRosa H / Gluc M / Jomaa A / Mattei S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Nature / Year: 2026
Title: SNOR promotes translation restart after dormancy.
Authors: Maciej Gluc / Higor Rosa / Maria Bozko / Lesley A Turner / Cassidy R Prince / Yelena Peskova / Heather A Feaga / Kathleen L Gould / Simone Mattei / Ahmad Jomaa /
Abstract: Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis. How inactive eukaryotic ribosomes are reactivated when nutrients return remains ...Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis. How inactive eukaryotic ribosomes are reactivated when nutrients return remains unclear. Here, using high-resolution in situ cryo-electron tomography in Schizosaccharomyces pombe, we identify SNOR, an SBDS domain-containing ribosome-associated factor that binds at the peptidyl transferase centre and contacts the hypusinated loop of eIF5A during glucose depletion-induced dormancy. Rather than acting as a canonical hibernation factor, SNOR licenses dormant ribosomes for rapid translational restart. Upon glucose repletion, SNOR and eIF5A act together to promote efficient recovery of polysomes and exit from dormancy. These findings define a stress-responsive ribosome restart module that couples carbon-source limitation to surveillance of the ribosomal active site and reactivation of protein synthesis.
History
DepositionJul 10, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54353.png

Downloads & links

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Map

FileDownload / File: emd_54353.map.gz / Format: CCP4 / Size: 181 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFiltered Sharpened map generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose starvation (subset Tethered to the Outer mitochondrial membrane)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.93 Å/pix.
x 362 pix.
= 699.746 Å		1.93 Å/pix.
x 362 pix.
= 699.746 Å		1.93 Å/pix.
x 362 pix.
= 699.746 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.933 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00168
Minimum - Maximum-0.0052784854 - 0.008412189
Average (Standard dev.)0.000017922364 (±0.00045682146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions362362362
Spacing362362362
CellA=B=C: 699.746 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Denoised map generated by M from in situ...

Fileemd_54353_additional_1.map
AnnotationDenoised map generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose starvation (subset Tethered to the Outer mitochondrial membrane)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 generated by M from in situ...

Fileemd_54353_half_map_1.map
AnnotationHalf-map 1 generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose starvation (subset Tethered to the Outer mitochondrial membrane)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 generated by M from in situ...

Fileemd_54353_half_map_2.map
AnnotationHalf-map 2 generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose starvation (subset Tethered to the Outer mitochondrial membrane)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In situ Hibernating Ribosomes from Schizosaccharomyces pombe cult...

EntireName: In situ Hibernating Ribosomes from Schizosaccharomyces pombe cultured under 7-day glucose depletion conditions
Components
  • Complex: In situ Hibernating Ribosomes from Schizosaccharomyces pombe cultured under 7-day glucose depletion conditions

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Supramolecule #1: In situ Hibernating Ribosomes from Schizosaccharomyces pombe cult...

SupramoleculeName: In situ Hibernating Ribosomes from Schizosaccharomyces pombe cultured under 7-day glucose depletion conditions
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Outer mitochondrial membrane tethered ribosomes
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

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 3.34 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: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.09) / Number subtomograms used: 12174
ExtractionNumber tomograms: 78 / Number images used: 20946 / Software - Name: Warp (ver. 1.09)
CTF correctionSoftware - Name: Warp (ver. 1.09) / Details: 3D CTF Estimation done in Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion (Refine) + M (PPoses)
FSC plot (resolution estimation)

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