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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: Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes.
Authors: Andre Schwarz / Mara Mueller / Helene Will / Lea Dietrich / Stefano L Giandomenico / Georgi Tushev / Ina Bartnik / Iskander Khusainov / Claudia M Fusco / Erin M Schuman /
Abstract: Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the ...Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the formation of inactive ribosome-ribosome clusters (disomes). We used cryo-electron tomography (cryo-ET) to visualize ribosomes in situ and observed that this ribosome dimerization was mediated by a homotypic interaction of the ribosomal RNA (rRNA) expansion segment ES31Lb. ES31Lb interactions were both necessary and sufficient for disome formation and conferred a growth advantage and stress resistance to brain cells. ES31Lb is predicted to homodimerize in ~20% of chordates, including variants in both chicken and human. Cryo-ET analysis of chicken tetrasomes revealed an interaction between ES31Lb and ES9La. Thus, in animal cells, translation regulation can use a flexible component of the protein synthesis machinery-rRNA expansion segments.
History
DepositionOct 15, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 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

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 5.364 Å
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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
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Half map: #1

Fileemd_55384_half_map_1.map
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Half map: #2

Fileemd_55384_half_map_2.map
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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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