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- EMDB-55183: 50S ribosomal subunit from RimM-WT with RsfS (+H68) -

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Basic information

Entry
Database: EMDB / ID: EMD-55183
Title50S ribosomal subunit from RimM-WT with RsfS (+H68)
Map data50S ribosomal subunit from RimM wildtype
Sample
  • Complex: 50S ribosomal subunit from RimM-WT with RsfS (+H68)
KeywordsRibosome assembly / RimM / initiation factor IF1 / initiation factor IF3 / anti-association / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHassan AH / Demo G
Funding support Czech Republic, United States, 4 items
OrganizationGrant numberCountry
Czech Science Foundation26-20643S Czech Republic
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM134931 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139202 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AG082005 United States
CitationJournal: bioRxiv / Year: 2026
Title: Mechanistic insights into recovery from growth arrest.
Authors: Ahmed Hassan / Yuko Nakano / Howard Gamper / Isao Masuda / Matyas Pinkas / Sathya Nagarajan / Jonathan Dworkin / Gregor Blaha / Ya-Ming Hou / Gabriel Demo /
Abstract: Bacteria survive hostile conditions in clinically relevant conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an Δ strain, which ...Bacteria survive hostile conditions in clinically relevant conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an Δ strain, which exhibits a prolonged growth arrest, as a model to investigate how bacteria recover from this arrested state and restore protein synthesis. RimM is a conserved ribosome maturation factor for the 3'-major (head) domain of the 16S rRNA within the bacterial 30S subunit. The loss of RimM causes a significantly longer delay in recovery than other 30S maturation factors, including RbfA - the presumed primary factor in 30S maturation. Cryo-EM analysis of Δ ribosomes revealed a delayed recruitment of ribosomal proteins to the 30S head domain and increased occupancy of the initiation factors IF1 and IF3, as well as recruitment of the silencing factor RsfS to the 50S subunit. These coordinated changes provide a safeguarding mechanism to block the assembly of premature 70S ribosomes. Notably, while the delayed 30S assembly in Δ reduces the activity of global protein synthesis during the recovery phase, bacteria attempt to compensate for this deficiency by producing higher levels of the ribosomal machinery, indicating a programmatic change in energy allocation to generate the ribosome machinery. These findings highlight the importance of the RimM-assisted assembly of the ribosomal head domain for bacterial recovery from growth arrest.
History
DepositionSep 25, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55183.png

Downloads & links

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Map

FileDownload / File: emd_55183.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation50S ribosomal subunit from RimM wildtype
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 400.32 Å		0.83 Å/pix.
x 480 pix.
= 400.32 Å		0.83 Å/pix.
x 480 pix.
= 400.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-8.172846 - 24.067454999999999
Average (Standard dev.)0.007030696 (±1.1303346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 400.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: 50S ribosomal subunit from RimM wildtype

Fileemd_55183_half_map_1.map
Annotation50S ribosomal subunit from RimM wildtype
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 50S ribosomal subunit from RimM wildtype

Fileemd_55183_half_map_2.map
Annotation50S ribosomal subunit from RimM wildtype
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 50S ribosomal subunit from RimM-WT with RsfS (+H68)

EntireName: 50S ribosomal subunit from RimM-WT with RsfS (+H68)
Components
  • Complex: 50S ribosomal subunit from RimM-WT with RsfS (+H68)

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Supramolecule #1: 50S ribosomal subunit from RimM-WT with RsfS (+H68)

SupramoleculeName: 50S ribosomal subunit from RimM-WT with RsfS (+H68) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.1 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
10.0 mMMgCl2Magnesium chloride
100.0 mMNH4ClAmonium chloride
0.5 mMEDTAEDTA
6.0 mM2-MercaptoethanolBME
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9710 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1469122
CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wde

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 11115
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN (ver. 9.11)
Final 3D classificationSoftware - Name: FREALIGN (ver. 9.11)

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