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- EMDB-53761: Map of M. pneumoniae 30S iT-TC (stable) in fidaxomicin-treated cells -

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Basic information

Entry
Database: EMDB / ID: EMD-53761
TitleMap of M. pneumoniae 30S iT-TC (stable) in fidaxomicin-treated cells
Map data
Sample
  • Cell: Mycoplasma pneumoniae M129-B7
Keywordsribosome / TRANSLATION
Function / homology
Function and homology information


ribosome disassembly / DNA-templated transcription termination / translation initiation factor activity / transcription antitermination / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis ...ribosome disassembly / DNA-templated transcription termination / translation initiation factor activity / transcription antitermination / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / protein dimerization activity / rRNA binding / ribonucleoprotein complex / structural constituent of ribosome / ribosome / translation / DNA-binding transcription factor activity / mRNA binding / regulation of DNA-templated transcription / magnesium ion binding / DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / Translation initiation factor 3, conserved site / Initiation factor 3 signature. / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 ...DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / Translation initiation factor 3, conserved site / Initiation factor 3 signature. / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / : / : / : / NusA-like second KH domain / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like first KH domain / Transcription termination/antitermination protein NusA, bacterial / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Type-1 KH domain profile. / Ribosomal protein S14, type Z / S1 domain profile. / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / Ribosomal protein S1-like RNA-binding domain / S1 domain / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / DNA-directed RNA polymerase, subunit beta-prime / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S9, bacterial/plastid / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / RNA polymerase Rpb1, clamp domain superfamily / Ribosomal protein S16 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 2 / Ribosomal protein S15, bacterial-type / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, funnel domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / Ribosomal protein S6 / Ribosomal protein S6 / RNA polymerase, RBP11-like subunit / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS21 / Probable DNA-directed RNA polymerase subunit delta / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS20 / DNA-directed RNA polymerase subunit beta' / Small ribosomal subunit protein bS18 ...Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS21 / Probable DNA-directed RNA polymerase subunit delta / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS20 / DNA-directed RNA polymerase subunit beta' / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS10 / Transcription termination/antitermination protein NusA / DNA-directed RNA polymerase subunit beta / Translation initiation factor IF-3 / DNA-directed RNA polymerase subunit alpha / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Translation initiation factor IF-1 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17
Similarity search - Component
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 9.5 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_53761.png

Downloads & links

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Map

FileDownload / File: emd_53761.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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Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0015
Minimum - Maximum-0.0017834295 - 0.016782956
Average (Standard dev.)0.000014689956 (±0.00054281607)
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_53761_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_53761_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: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 1689
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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