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- EMDB-53849: Map of E. coli 50S membrane complex with SecYEG -

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Basic information

Entry
Database: EMDB / ID: EMD-53849
TitleMap of E. coli 50S membrane complex with SecYEG
Map data
Sample
  • Cell: Membrane-attached ribosome from Escherichia coli BW25113 with density corresponding to the SecYEG translocon
Keywordsribosome / TRANSLATION
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 28.9 Å
AuthorsDobbs JM / Jensen RK / Mahamid J
Funding support United States, Denmark, 2 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative2021-234620 United States
Independent Research Fund Denmark - Medical Sciences0106-00010A Denmark
CitationJournal: Cell / Year: 2026
Title: Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries.
Authors: Joseph M Dobbs / Rasmus K Jensen / Julia Mahamid /
Abstract: Translation is a central process in gene expression. Its regulation is complex, depends on factors that include cell state and the subcellular environment, and is subject to modulation via crosstalk ...Translation is a central process in gene expression. Its regulation is complex, depends on factors that include cell state and the subcellular environment, and is subject to modulation via crosstalk to processes such as transcription or translocation. Here, we used cryo-electron tomography of native and antibiotic-perturbed Mycoplasma pneumoniae cells to resolve 140 maps that recapitulate bacterial translation during the initiation, elongation, and recycling phases. We visualized multiple transcription-translation complexes, allowing us to propose a threading-based translation reinitiation mechanism and to provide structural evidence for a long-hypothesized supercomplex that coordinates transcription, translation, and membrane attachment. We resolved abundant membrane-associated large ribosomal subunits and suggest that dissociation from membranes depends on the conditional initiation of new translation, consistent with a potentially conserved mechanism in mammalian cells. This work visualizes the multilayered control of bacterial translation and demonstrates the power of in-cell structural biology to investigate regulatory circuits in gene expression.
History
DepositionMay 19, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53849.png

Downloads & links

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Map

FileDownload / File: emd_53849.map.gz / Format: CCP4 / Size: 23.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
5 Å/pix.
x 184 pix.
= 920. Å		5 Å/pix.
x 184 pix.
= 920. Å		5 Å/pix.
x 184 pix.
= 920. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0169
Minimum - Maximum-0.009890652 - 0.045409407
Average (Standard dev.)0.00061687536 (±0.00447976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions184184184
Spacing184184184
CellA=B=C: 920.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53849_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53849_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane-attached ribosome from Escherichia coli BW25113 with den...

EntireName: Membrane-attached ribosome from Escherichia coli BW25113 with density corresponding to the SecYEG translocon
Components
  • Cell: Membrane-attached ribosome from Escherichia coli BW25113 with density corresponding to the SecYEG translocon

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Supramolecule #1: Membrane-attached ribosome from Escherichia coli BW25113 with den...

SupramoleculeName: Membrane-attached ribosome from Escherichia coli BW25113 with density corresponding to the SecYEG translocon
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW25113
Details: Treated with 0.2mg/ml chloramphenicol (Cm) for 15 minutes at 37 degrees Celsius

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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: 7.4
GridModel: Quantifoil R1/4 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 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: 28.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 859
ExtractionNumber tomograms: 294 / Number images used: 605500 / Software - Name: Warp (ver. 1.09)
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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