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- EMDB-58190: Subtomogram average of E. scolopes ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-58190
TitleSubtomogram average of E. scolopes ribosome
Map data
Sample
  • Cell: Vibrio fischeri within the light organ crypt of Euprymna scolopes
Keywordscytoplasm / translation / ribonucleoprotein complex / RIBOSOME
Biological speciesEuprymna scolopes (invertebrata)
Methodsubtomogram averaging / cryo EM / Resolution: 6.6 Å
AuthorsSo-Last MGF / Allegretti MA
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF-721-2024European Union
Medical Research Council (MRC, United Kingdom)MC_UP_1201/29 United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: Nanoscale imaging of native symbiotic animal tissue using a multimodal large volume imaging pipeline for cryo-electron tomography
Authors: Gundlach KA / Schiotz OH / Ladinsky M / Raimann C / Rheinberger M / Beck F / Gunduz B / Langelaan R / Rucklin M / Limpens RW / Ruby EG / McFall-Ngai M / Plitzko JM / Briegel A
History
DepositionMay 19, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58190.png

Downloads & links

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Map

FileDownload / File: emd_58190.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 334 pix.
= 501. Å		1.5 Å/pix.
x 334 pix.
= 501. Å		1.5 Å/pix.
x 334 pix.
= 501. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00133
Minimum - Maximum-0.0027266927 - 0.005515206
Average (Standard dev.)0.000024983614 (±0.0003264826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions334334334
Spacing334334334
CellA=B=C: 501.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58190_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_58190_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58190_half_map_2.map
Projections & Slices
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Sample components

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Entire : Vibrio fischeri within the light organ crypt of Euprymna scolopes

EntireName: Vibrio fischeri within the light organ crypt of Euprymna scolopes
Components
  • Cell: Vibrio fischeri within the light organ crypt of Euprymna scolopes

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Supramolecule #1: Vibrio fischeri within the light organ crypt of Euprymna scolopes

SupramoleculeName: Vibrio fischeri within the light organ crypt of Euprymna scolopes
type: cell / ID: 1 / Parent: 0
Details: Symbiotic Vibrio fischeri cells within the crypt epithelium of the juvenile Hawaiian bobtail squid (Euprymna scolopes) light organ. Animals were colonised, dissected, and high pressure ...Details: Symbiotic Vibrio fischeri cells within the crypt epithelium of the juvenile Hawaiian bobtail squid (Euprymna scolopes) light organ. Animals were colonised, dissected, and high pressure frozen. The light organ region containing colonised crypts was localised by correlative cryo fluorescence microscopy and microCT, and cryo lamellae of the host symbiont interface were prepared by cryo FIB lift out for cryo electron tomography. Sample preparation is described in Gundlach, Schioetz et al., bioRxiv 2025.11.30.691379.
Source (natural)Organism: Euprymna scolopes (invertebrata)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7
VitrificationCryogen name: OTHER
DetailsWe reprocessed the data from https://www.biorxiv.org/content/10.1101/2025.11.30.691379v1.abstract

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 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: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M (ver. 2.0.0dev36) / Number subtomograms used: 10334
ExtractionNumber tomograms: 37 / Number images used: 10334 / Software - Name: Warp
Software - details: NOTE: we used easymode (github.com/mgflast/easymode) and Ais (github.com/bionanopatterning/Ais)
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0-dev)

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