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- EMDB-54958: Subtomogram average of the C. thermophilum 80S ribosome - eIF5a bound -

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Basic information

Entry
Database: EMDB / ID: EMD-54958
TitleSubtomogram average of the C. thermophilum 80S ribosome - eIF5a bound
Map datasubtomogram average of the C. thermophilum 80S ribosome with eIF5a
Sample
  • Cell: FIB milled C. thermophilum hyphae
Keywordseukaryotic ribosome / 80S / thermophile / eIF5a / hibernation / RIBOSOME
Biological speciesThermochaetoides thermophila (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 8.2 Å
AuthorsKopetschke S / Filbeck S / Pfeffer S
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC)European Union
German Federal Ministry for Education and Research Germany
CitationJournal: To Be Published
Title: Cold-induced structural remodeling of the translation machinery visualized in situ by cellular cryo-ET
Authors: Kopetschke S / Flibeck S / Pfeffer S
History
DepositionSep 2, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54958.png

Downloads & links

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Map

FileDownload / File: emd_54958.map.gz / Format: CCP4 / Size: 68.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of the C. thermophilum 80S ribosome with eIF5a
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.67 Å/pix.
x 262 pix.
= 699.802 Å		2.67 Å/pix.
x 262 pix.
= 699.802 Å		2.67 Å/pix.
x 262 pix.
= 699.802 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.671 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0018
Minimum - Maximum-0.0031848678 - 0.0100371465
Average (Standard dev.)0.000016491034 (±0.00050488184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions262262262
Spacing262262262
CellA=B=C: 699.802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half 1

Fileemd_54958_half_map_1.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2

Fileemd_54958_half_map_2.map
Annotationhalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FIB milled C. thermophilum hyphae

EntireName: FIB milled C. thermophilum hyphae
Components
  • Cell: FIB milled C. thermophilum hyphae

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Supramolecule #1: FIB milled C. thermophilum hyphae

SupramoleculeName: FIB milled C. thermophilum hyphae / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
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: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M (ver. 1.0.9) / Number subtomograms used: 19996
ExtractionNumber tomograms: 79 / Number images used: 115371 / Software - Name: PyTom (ver. v0.971)
CTF correctionType: NONE
Final angle assignmentType: PROJECTION MATCHING

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