[English] 日本語
Yorodumi
- EMDB-72256: Pseudomonas aeruginosa 50S ribosome bound to RsfS (base map) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72256
TitlePseudomonas aeruginosa 50S ribosome bound to RsfS (base 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: 2.29 Å
AuthorsFindlay JL / Kanik M / Gauvin CC / Franklin MJ / Lawrence CM
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R41 GM148117 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R41 GM153173 United States
National Science Foundation (NSF, United States)DBI-1828765 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM140963 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI154171 United States
CitationJournal: To Be Published
Title: RsfS Prevents 70S Formation During Active Cell Growth in P. aeruginosa
Authors: Findlay JL / Kanik M / Franklin MJ / Lawrence CM
History
DepositionAug 21, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72256.png

Downloads & links

-
Map

FileDownload / File: emd_72256.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.673 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-24.698101000000001 - 50.217545000000001
Average (Standard dev.)-0.002553784 (±0.9481132)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_72256_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_72256_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72256_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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.

-
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

+
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: 1 / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.1) / Number images used: 452165
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: 2 / Avg.num./class: 550000 / Software - Name: cryoSPARC (ver. v4.7.1)
Details: The two final classes for the base map were plus and minus RsfS. Further classification of the L1 stalk region followed by local refinement resulted in another four classes for each of the two base map classes.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

7unw

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more