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- EMDB-55378: Nutrient deprived rat neuronal 80S ribosome state - hibernating II -

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Basic information

Entry
Database: EMDB / ID: EMD-55378
TitleNutrient deprived rat neuronal 80S ribosome state - hibernating II
Map data
Sample
  • Cell: Primary cultured rat hippocampal neurons
KeywordsComplex / Translation / Neuron / RIBOSOME
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 8.4 Å
AuthorsSchwarz A / Schuman EM
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_55378.png

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Map

FileDownload / File: emd_55378.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 168 pix.
= 450.576 Å		2.68 Å/pix.
x 168 pix.
= 450.576 Å		2.68 Å/pix.
x 168 pix.
= 450.576 Å

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Voxel sizeX=Y=Z: 2.682 Å
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Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-0.4500332 - 1.057092
Average (Standard dev.)0.0064063766 (±0.058078855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 450.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55378_msk_1.map
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Half map: #1

Fileemd_55378_half_map_1.map
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Half map: #2

Fileemd_55378_half_map_2.map
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Sample components

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Entire : Primary cultured rat hippocampal neurons

EntireName: Primary cultured rat hippocampal neurons
Components
  • Cell: Primary cultured rat hippocampal neurons

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Supramolecule #1: Primary cultured rat hippocampal neurons

SupramoleculeName: Primary cultured rat hippocampal neurons / type: cell / ID: 1 / Parent: 0 / Details: nutrient deprived (E4 Buffer)
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: brain / Tissue: hippocampus

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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: 7.4
Details: 120 mM NaCl, 3 mM KCl, 10 mM D-Glucose, 10 mM HEPES (1 M solution, Gibco 15630-056), pH adjusted to 7.4 with 1 M NaOH, supplemented with 2 mM MgSO4 and 2 mM CaCl2 on the day of the ...Details: 120 mM NaCl, 3 mM KCl, 10 mM D-Glucose, 10 mM HEPES (1 M solution, Gibco 15630-056), pH adjusted to 7.4 with 1 M NaOH, supplemented with 2 mM MgSO4 and 2 mM CaCl2 on the day of the experiment), lacking the amino acids, vitamins and other nutrients present in B27 and GlutaMAX
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.
DetailsThis sample was grown on EM grids, coated with poly-D-lysine, at a density of 140,000 cells/ml in E4 buffer (nutrient deprived)

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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: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1), M (ver. 1.0.9)) / Number subtomograms used: 3903
ExtractionNumber tomograms: 341 / Number images used: 183530
Reference model: low resolution STA of manually picked particles
Method: STOPGAP template matching / Software - Name: Warp (ver. 1.0.9) / Details: picked in deconvolved tomograms
CTF correctionSoftware: (Name: Warp (ver. 1.0.9), RELION (ver. 3.1)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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