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- EMDB-53764: Map of M. pneumoniae 50S membrane complex in fidaxomicin-treated cells -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-53764
TitleMap of M. pneumoniae 50S membrane complex in fidaxomicin-treated cells
Map data
Sample
  • Cell: Mycoplasma pneumoniae M129-B7
Keywordsribosome / TRANSLATION
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 8.8 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 14, 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_53764.png

Downloads & links

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Map

FileDownload / File: emd_53764.map.gz / Format: CCP4 / Size: 103 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.)
2 Å/pix.
x 300 pix.
= 600. Å		2 Å/pix.
x 300 pix.
= 600. Å		2 Å/pix.
x 300 pix.
= 600. Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00129
Minimum - Maximum-0.0035108232 - 0.016147628
Average (Standard dev.)0.000036335303 (±0.00058831024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 600.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53764_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_53764_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Mycoplasma pneumoniae M129-B7

EntireName: Mycoplasma pneumoniae M129-B7
Components
  • Cell: Mycoplasma pneumoniae M129-B7

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Supramolecule #1: Mycoplasma pneumoniae M129-B7

SupramoleculeName: Mycoplasma pneumoniae M129-B7 / type: cell / ID: 1 / Parent: 0
Details: Treated with 0.4mg/ml fidaxomicin (FID) for 30 minutes at 37 degrees Celsius
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Details: Treated with 0.4mg/ml fidaxomicin (FID) for 30 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 R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE
DetailsTreated with 0.4mg/ml fidaxomicin (FID) for 30 minutes at 37 degrees Celsius

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 53000 / 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: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 2035
ExtractionNumber tomograms: 100 / Number images used: 259200 / 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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