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- EMDB-56861: In situ ribosome from HeLa cells -

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Basic information

Entry
Database: EMDB / ID: EMD-56861
TitleIn situ ribosome from HeLa cells
Map dataOutput from postprocess in RELION
Sample
  • Cell: Wild type HeLa cells
KeywordsIn situ / ribosome / EasyGrid
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 6.8 Å
AuthorsGemin O / Babenko A / Papp G
Funding support Germany, 1 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND Germany
CitationJournal: Nat Methods / Year: 2026
Title: EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.
Authors: Olivier Gemin / Victor Armijo / Léa Lecomte / Michael Hons / Thibault Deckers / Caroline Bissardon / Christopher Rossi / Kévin Lauzier / Robert Janocha / Franck Felisaz / Jérémy Sinoir / ...Authors: Olivier Gemin / Victor Armijo / Léa Lecomte / Michael Hons / Thibault Deckers / Caroline Bissardon / Christopher Rossi / Kévin Lauzier / Robert Janocha / Franck Felisaz / Jérémy Sinoir / Romain Linares / Anastasiia Babenko / Kirill Kovalev / Irina Prokhorova / Iskander Khusainov / Claudia Schreiner / Olga Kolesnikova / Veijo T Salo / Sarah Schneider / Matthew W Bowler / Georg Wolff / Wojciech P Galej / Julia Mahamid / Christoph W Müller / Kristina Djinovic Carugo / Sebastian Eustermann / Simone Mattei / Florent Cipriani / Gergely Papp /
Abstract: Optimized sample preparation is essential for imaging biological macromolecules in their native state using single-particle cryo-electron microscopy (cryo-EM) or in situ cryo-electron tomography ...Optimized sample preparation is essential for imaging biological macromolecules in their native state using single-particle cryo-electron microscopy (cryo-EM) or in situ cryo-electron tomography (cryo-ET). Here we present EasyGrid, a modular, automated platform designed to streamline and standardize cryo-EM/ET sample preparation. EasyGrid integrates in-line plasma treatment of the sample support, microfluidic dispensing, blot-less sample spreading, jet-based vitrification and grid quality control via light interferometry. We demonstrate its effectiveness by preparing grids for multiple purified macromolecular complexes and resolving their structures with cryo-EM. Additionally, EasyGrid achieves improved vitrification of large mammalian cells compared to conventional plunge-freezing. By enabling systematic and high-throughput optimization, EasyGrid provides a robust and time-saving solution for both structural and cellular cryo-EM applications.
History
DepositionFeb 20, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56861.png

Downloads & links

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Map

FileReleased
AnnotationOutput from postprocess in RELION
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 346 pix.
= 680.928 Å		1.97 Å/pix.
x 346 pix.
= 680.928 Å		1.97 Å/pix.
x 346 pix.
= 680.928 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.968 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00128
Minimum - Maximum-0.001269031 - 0.004010289
Average (Standard dev.)0.000011649269 (±0.0002107236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions346346346
Spacing346346346
CellA=B=C: 680.92804 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56861_msk_1.map
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Additional map: Denoised by M

Fileemd_56861_additional_1.map
AnnotationDenoised by M
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Half map: Half map 1

Fileemd_56861_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Histogram

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Half map: Half map 2

Fileemd_56861_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : Wild type HeLa cells

EntireName: Wild type HeLa cells
Components
  • Cell: Wild type HeLa cells

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Supramolecule #1: Wild type HeLa cells

SupramoleculeName: Wild type HeLa cells / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa

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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: 7.5
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: 2.63 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 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: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Warp, RELION (ver. 4)) / Number subtomograms used: 10648
ExtractionNumber tomograms: 33 / Number images used: 10648 / Software - Name: Warp
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationAvg.num./class: 10648
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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