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- EMDB-56682: In situ ribosome structure from environmental sample of Pseudo-ni... -

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Basic information

Entry
Database: EMDB / ID: EMD-56682
TitleIn situ ribosome structure from environmental sample of Pseudo-nitzschia
Map dataFiltered map after FSC estimation.
Sample
  • Cell: Pseudo-nitzschia sp.
KeywordsRibosome / Environmental Sample / Diatom / RIBOSOMAL PROTEIN
Biological speciesPseudo-nitzschia sp. (Diatom)
Methodsubtomogram averaging / cryo EM / Resolution: 28.65 Å
AuthorsLeisch N / Pyle E
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP2416 project number BE 5417/2-1 Germany
CitationJournal: bioRxiv / Year: 2026
Title: An Advanced Mobile Laboratory to enable field-based microbial ecology and cell biology across scales.
Authors: N Leisch / S Baars / T Beavis / P Bertucci / C Bhickta / M Bonadonna / C M Brannon / L Burgués-Palau / P Cherek / F Chevalier / J Decelle / M Demulder / G Dey / O Dudin / E Duke / B D Engel ...Authors: N Leisch / S Baars / T Beavis / P Bertucci / C Bhickta / M Bonadonna / C M Brannon / L Burgués-Palau / P Cherek / F Chevalier / J Decelle / M Demulder / G Dey / O Dudin / E Duke / B D Engel / E Flaum / S Flori / B Gallet / P Guichard / A Halavatyi / V Hamel / M Jacobovitz / C Juery / M Laporte / S Mattei / F Mikus / K Mocaer / K Moog / M Olivetta / M Pavie / R Pepperkok / A Perez-Boerema / L Planat / M Prakash / E W Pyle / C R Rhodes / I Romero-Brey / P Ronchi / H Rosa / A Rubio Ramos / C Saint-Donat / Y Schwab / H Shah / A M Steyer / A Svetlove / G Toullec / F Vincent / T Wiegand / W Wietrzynski / D Yee / S Zwahlen /
Abstract: Microbial biodiversity is central to ecosystem function, yet mechanistic insights into the cell biology of environmental organisms remain limited. The underlying challenges are twofold: most microbes ...Microbial biodiversity is central to ecosystem function, yet mechanistic insights into the cell biology of environmental organisms remain limited. The underlying challenges are twofold: most microbes remain uncultivable, and a persistent gap exists between field sampling and laboratory analyses. Here, we introduce the Advanced Mobile Laboratory (AML), a field-deployable platform that integrates confocal microscopy, image-enabled cell sorting, and cryo-preparation for expansion and electron microscopy. This setup enables immediate, standardized processing and analysis of environmental communities directly at the sampling site. We demonstrate its capability using marine eukaryotic plankton, showing how the AML enables multiscale investigations, from live imaging of natural communities to enabling ultrastructural and single-cell omics analyses, while minimizing sample degradation and enabling on-site experimentation. By bringing high-end sample preparation and analytical capacity into the field, the AML enables studying life in its natural context to mechanistically understand life's diversity in the environment.
History
DepositionFeb 11, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56682.png

Downloads & links

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Map

FileDownload / File: emd_56682.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFiltered map after FSC estimation.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.09 Å/pix.
x 84 pix.
= 679.392 Å		8.09 Å/pix.
x 84 pix.
= 679.392 Å		8.09 Å/pix.
x 84 pix.
= 679.392 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0175
Minimum - Maximum-0.022441559 - 0.047934942
Average (Standard dev.)0.00029944192 (±0.0044760727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions848484
Spacing848484
CellA=B=C: 679.392 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56682_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Map filtered by local resolution.

Fileemd_56682_additional_1.map
AnnotationMap filtered by local resolution.
Projections & Slices
AxesZYX

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Additional map: Map denoised by M.

Fileemd_56682_additional_2.map
AnnotationMap denoised by M.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Unfiltered half map 1.

Fileemd_56682_half_map_1.map
AnnotationUnfiltered half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 2.

Fileemd_56682_half_map_2.map
AnnotationUnfiltered half map 2.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudo-nitzschia sp.

EntireName: Pseudo-nitzschia sp. (Diatom)
Components
  • Cell: Pseudo-nitzschia sp.

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Supramolecule #1: Pseudo-nitzschia sp.

SupramoleculeName: Pseudo-nitzschia sp. / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Pseudo-nitzschia sp. (Diatom)

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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
DetailsCell extracted from natural environment.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 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: 28.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number subtomograms used: 388
ExtractionNumber tomograms: 2 / Number images used: 643 / Software - Name: Warp
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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