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- EMDB-72274: Pseudomonas aeruginosa 50S ribosome bound to RsfS (L7/L12 Stalk l... -

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Basic information

Entry
Database: EMDB / ID: EMD-72274
TitlePseudomonas aeruginosa 50S ribosome bound to RsfS (L7/L12 Stalk local map)
Map data
Sample
  • Complex: Ribosome fraction isolated from wild type P. aeruginosa cells during exponential phase growth
Keywords50S Ribosome / ribosome silencing factor during starvation / RsfS / Pseudomonas aeruginosa / Ribosome
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsFindlay JL / Lawrence CM / Kanik M / Franklin MJ / Gauvin CC
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH 1R41GM148117 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R41GM153173 United States
National Science Foundation (NSF, United States)NSF DBI-1828765 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH P30GM140963 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R21 AI154171 United States
CitationJournal: To Be Published
Title: RsfS Prevents 70S Formation During Active Cell Growth in P. aeruginosa
Authors: Findlay JL / Lawrence CM / Kanik M / Franklin MJ
History
DepositionAug 22, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72274.png

Downloads & links

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Map

FileDownload / File: emd_72274.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 696 pix.
= 468.408 Å		0.67 Å/pix.
x 696 pix.
= 468.408 Å		0.67 Å/pix.
x 696 pix.
= 468.408 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.673 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.44710448 - 0.7878329
Average (Standard dev.)-0.0002078054 (±0.003469055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions696696696
Spacing696696696
CellA=B=C: 468.408 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72274_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_72274_half_map_1.map
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Half map: #1

Fileemd_72274_half_map_2.map
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Sample components

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Entire : Ribosome fraction isolated from wild type P. aeruginosa cells dur...

EntireName: Ribosome fraction isolated from wild type P. aeruginosa cells during exponential phase growth
Components
  • Complex: Ribosome fraction isolated from wild type P. aeruginosa cells during exponential phase growth

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Supramolecule #1: Ribosome fraction isolated from wild type P. aeruginosa cells dur...

SupramoleculeName: Ribosome fraction isolated from wild type P. aeruginosa cells during exponential phase growth
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 1.49 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

Concentration2.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H12ClNO3Tris-HCL
300.0 mMNH4ClAmmonium Chloride
10.5 mMMg(CH3COO)2Manesium acetate
0.5 mMC10H16N2O8EDTA
3.0 mMC2H6OSbeta-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time: 5 seconds Blot force: 3.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 13721 / Average exposure time: 5.0 sec. / Average electron dose: 54.3 e/Å2 / Details: 50 frames per movie at 0.1 seconds per frame
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1665000
CTF correctionSoftware - Name: cryoSPARC (ver. v4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Details: Multi class ab initio was used to generate three initial models for each major ribosome assembly state.
Final reconstructionNumber classes used: 2 / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.1)
Details: Local refinement was done using a mask focused on the L7/L12 stalk. Particle subtraction was performed prior to local refinement.
Number images used: 126369
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. v4.7.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v4.7.1)
Final 3D classificationNumber classes: 8 / Avg.num./class: 56500 / Software - Name: cryoSPARC (ver. v4.7.1)
Details: Classification was done using a focused maks on the L7/L12 stalk. Only two classes were used that showed most complete density for ribosomal proteins L10 and L11.

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Atomic model buiding 1

Initial modelPDB ID:

7unw


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitially, each chain of the 7UNW 50S subunit was rigid body fit into the experimental map. Occasionally Alpha fold 2 generated models of individual chains were used instead. Models were then refined in phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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