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- EMDB-52599: Ribosome STA of particles classified by pytom-match-pick using th... -

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Basic information

Entry
Database: EMDB / ID: EMD-52599
TitleRibosome STA of particles classified by pytom-match-pick using the dual-constraint strategy.
Map dataRibosome STA bound to ER-microsomes from 10 tilt-series for particle localization validation
Sample
  • Complex: 80S ER-bound ribosome on extracted microsomes
Keywordser-microsome / method development / template matching / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 14.77 Å
AuthorsChaillet ML / Forster F / Roet S / Veltkmap RC
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101113464European Union
CitationJournal: To Be Published
Title: Ribosome STA of particles classified by pytom-match-pick using the base extraction threshold.
Authors: Chaillet ML / Forster F / Roet S / Veltkmap RC
History
DepositionJan 23, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52599.png

Downloads & links

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Map

FileDownload / File: emd_52599.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRibosome STA bound to ER-microsomes from 10 tilt-series for particle localization validation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.45 Å/pix.
x 120 pix.
= 413.76 Å		3.45 Å/pix.
x 120 pix.
= 413.76 Å		3.45 Å/pix.
x 120 pix.
= 413.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.448 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.37
Minimum - Maximum-0.39192063 - 1.1705892
Average (Standard dev.)0.047869734 (±0.18473165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 413.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Ribosome STA bound to ER-microsomes from 10 tilt-series...

Fileemd_52599_half_map_1.map
AnnotationRibosome STA bound to ER-microsomes from 10 tilt-series for particle localization validation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ribosome STA bound to ER-microsomes from 10 tilt-series...

Fileemd_52599_half_map_2.map
AnnotationRibosome STA bound to ER-microsomes from 10 tilt-series for particle localization validation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S ER-bound ribosome on extracted microsomes

EntireName: 80S ER-bound ribosome on extracted microsomes
Components
  • Complex: 80S ER-bound ribosome on extracted microsomes

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Supramolecule #1: 80S ER-bound ribosome on extracted microsomes

SupramoleculeName: 80S ER-bound ribosome on extracted microsomes / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.003 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1058
ExtractionNumber tomograms: 10 / Number images used: 1058
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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