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- EMDB-55376: Nutrient deprived rat neuronal 80S ribosome state - peptide bond ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55376
TitleNutrient deprived rat neuronal 80S ribosome state - peptide bond formation
Map data
Sample
  • Cell: Primary cultured rat hippocampal neurons
KeywordsComplex / Translation / Neuron / RIBOSOME
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 5.8 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: 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_55376.png

Downloads & links

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Map

FileDownload / File: emd_55376.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.682 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.6900745 - 1.5024258
Average (Standard dev.)0.0071033034 (±0.069736816)
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_55376_msk_1.map
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Half map: #1

Fileemd_55376_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55376_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 : 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: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1), M (ver. 1.0.9)) / Number subtomograms used: 18031
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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