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- EMDB-55384: 1 h nitrogen + carbon starved yeast-rat-hybrid hibernating disome -

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Basic information

Entry
Database: EMDB / ID: EMD-55384
Title1 h nitrogen + carbon starved yeast-rat-hybrid hibernating disome
Map data
Sample
  • Cell: Engineered yeast-rat-hybrid strain, S287C
KeywordsComplex / Translation / Neuron / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 15.2 Å
AuthorsSchwarz A / Schuman EM / Dietrich LT
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Molecular Biology Organization (EMBO)ALT 836-2020European Union
European Research Council (ERC)101054512European Union
CitationJournal: Science / Year: 2026
Title: rRNA expansion segments mediate the oligomerization of inactive animal ribosomes
Authors: Schwarz A / Schuman EM
History
DepositionOct 15, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55384.png

Downloads & links

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Map

FileDownload / File: emd_55384.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.36 Å/pix.
x 180 pix.
= 965.52 Å		5.36 Å/pix.
x 180 pix.
= 965.52 Å		5.36 Å/pix.
x 180 pix.
= 965.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.364 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.63
Minimum - Maximum-0.5027198 - 2.0623639
Average (Standard dev.)0.0064714947 (±0.14602436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 965.51996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55384_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55384_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55384_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Engineered yeast-rat-hybrid strain, S287C

EntireName: Engineered yeast-rat-hybrid strain, S287C
Components
  • Cell: Engineered yeast-rat-hybrid strain, S287C

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Supramolecule #1: Engineered yeast-rat-hybrid strain, S287C

SupramoleculeName: Engineered yeast-rat-hybrid strain, S287C / type: cell / ID: 1 / Parent: 0
Details: Grown in synthetic defined medium lacking leucine (SD -LEU) overnight, transfered to YPD (full medium), then nitrogen deprived in synthetic defined medium lacking nitrogen (SD -N) (Sigma ...Details: Grown in synthetic defined medium lacking leucine (SD -LEU) overnight, transfered to YPD (full medium), then nitrogen deprived in synthetic defined medium lacking nitrogen (SD -N) (Sigma Aldrich, Y1251 + Glucose) for 1 h
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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: 5.2
Details: synthetic defined medium lacking nitrogen (SD -N) (Sigma Aldrich, Y1251 + 2% (w/v) Glucose)
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 310 K / Instrument: LEICA EM GP / Details: 10s blotting time, Whatman filter paper #1.
DetailsThe yeast was grown in synthetic defined medium lacking LEU (as selection pressure) at 30 degree celcius 250 rpm overnight, transferred to YPD (full medium) at OD600=0.15, grown until OD600=0.5, then resuspended in synthetic defined medium lacking nitrogen (SD -N) (Sigma Aldrich, Y1251 + Glucose) for 1 h at 30 degree celcius 250 rpm. 3 ul of OD600=0.9 were applied to grids and plunge frozen

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 90.0 K / Max: 95.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.45 sec. / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 33000
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) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1), M (ver. 1.0.9)) / Number subtomograms used: 2923
ExtractionNumber tomograms: 66 / Number images used: 39149 / Reference model: stitched map of two 80S, low-pass filtered / Method: Geometric picking / Software - Name: Warp (ver. 1.0.9)
Details: First, a rough STA map was created using ~2k interactively picked particles, followed by GAPSTOP template matching and refinement of 80S monomers. Then, coordinates of neighboring ribosomes ...Details: First, a rough STA map was created using ~2k interactively picked particles, followed by GAPSTOP template matching and refinement of 80S monomers. Then, coordinates of neighboring ribosomes were displayed using python/napari, thresholded, and disome neighbors in the correct orientation were selected interactive into a new particle list. This particle list was then refined.
CTF correctionSoftware: (Name: Warp (ver. 1.0.9), RELION (ver. 3.1)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 15 / Software - Name: RELION (ver. 3.1) / Details: k=1
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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