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- EMDB-56963: Ribosome subtomogram average -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56963
TitleRibosome subtomogram average
Map data
Sample
  • Organelle or cellular component: COPI and COPII coats in Halo_Sec23A RPE-1 cells.
KeywordsRibosome
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 15.0 Å
AuthorsDownes KW / Nans A / Zanetti G
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-StG-2019 grant 852915European Union
CitationJournal: Biorxiv / Year: 2025
Title: Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites
Authors: Downes K / Flood J / Nans A / Van der Verren S / Audhya A / Zanetti G
History
DepositionFeb 27, 2026-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56963.png

Downloads & links

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Map

FileDownload / File: emd_56963.map.gz / Format: CCP4 / Size: 73.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.24 Å/pix.
x 268 pix.
= 600.32 Å		2.24 Å/pix.
x 268 pix.
= 600.32 Å		2.24 Å/pix.
x 268 pix.
= 600.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 40.0
Minimum - Maximum8.754723 - 71.680300000000003
Average (Standard dev.)66.189319999999995 (±15.825158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions268268268
Spacing268268268
CellA=B=C: 600.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_56963_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56963_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : COPI and COPII coats in Halo_Sec23A RPE-1 cells.

EntireName: COPI and COPII coats in Halo_Sec23A RPE-1 cells.
Components
  • Organelle or cellular component: COPI and COPII coats in Halo_Sec23A RPE-1 cells.

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Supramolecule #1: COPI and COPII coats in Halo_Sec23A RPE-1 cells.

SupramoleculeName: COPI and COPII coats in Halo_Sec23A RPE-1 cells. / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Halo tag added to endogenous site of Sec23A in RPE-1 cells, used to target lamella production by FIB-milling and tomograms positioning.
Source (natural)Organism: Homo sapiens (human) / Strain: Halo_Sec23A RPE-1 / Organelle: ERES

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 1.0 AU / Component - Formula: DMEM/F12
Component - Name: DMEM/F12, 10% FBS, L-glutamine, 1% Pen/Strep
StainingType: NONE / Material: Oregon Green-HaloTag Ligand
Details: Cells stained with 1 uL/mL Oregon Green-HaloTag Ligand
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 310 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 10.0 µm / Nominal defocus min: 7.0 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: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number subtomograms used: 16000
ExtractionNumber tomograms: 60 / Number images used: 16000 / Software - Name: RELION (ver. 5)
CTF correctionSoftware - Name: Warp / Details: WARP pipeline / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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