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- EMDB-54354: In situ Free Cytosolic Hibernating Ribosomes from S. pombe under ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54354
TitleIn situ Free Cytosolic 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 (free cytosolic subset)
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: 6.7 Å
AuthorsRosa H / Gluc M / Jomaa A / Mattei S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: To Be Published
Title: A novel eukaryotic ribosome factor promotes translation restart after dormancy
Authors: Gluc M / Rosa H / Bozko M / Prince CR / Turner LA / Feaga HA / Gould KL / Mattei S / Jomaa A
History
DepositionJul 10, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54354.png

Downloads & links

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Map

FileDownload / File: emd_54354.map.gz / Format: CCP4 / Size: 52.7 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 (free cytosolic subset)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.93 Å/pix.
x 240 pix.
= 463.92 Å		1.93 Å/pix.
x 240 pix.
= 463.92 Å		1.93 Å/pix.
x 240 pix.
= 463.92 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: 0.6
Minimum - Maximum-1.3813636 - 3.3763723
Average (Standard dev.)0.029493038 (±0.25872323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 463.91998 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_54354_additional_1.map
AnnotationDenoised map generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose starvation (free cytosolic subset)
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_54354_half_map_1.map
AnnotationHalf-map 1 generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose starvation (free cytosolic subset)
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_54354_half_map_2.map
AnnotationHalf-map 2 generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose starvation (free cytosolic subset)
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: Free cytosolic 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: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.09) / Number subtomograms used: 14006
ExtractionNumber tomograms: 78 / Number images used: 23009 / 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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