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- EMDB-52842: Cryo-ET of cryo-FIB milled P. urativorans grown at physiological ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52842
TitleCryo-ET of cryo-FIB milled P. urativorans grown at physiological conditions
Map dataRepresentative tomogram of cryo-FIB milled P. urativorans grown at physiological conditions
Sample
  • Cell: Tomogram of cryo-FIB milled Psychrobacter urativorans grown at physiological conditions
KeywordsPsychrobacter / physiological / ribosome
Biological speciesPsychrobacter urativorans (bacteria)
Methodelectron tomography / cryo EM
AuthorsKopetschke S / Pfeffer S
Funding supportEuropean Union, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Other private
Other private
CitationJournal: Nat Commun / Year: 2025
Title: Structurally heterogeneous ribosomes cooperate in protein synthesis in bacterial cells.
Authors: Karla Helena-Bueno / Sophie Kopetschke / Sebastian Filbeck / Lewis I Chan / Sonia Birsan / Arnaud Baslé / Maisie Hudson / Stefan Pfeffer / Chris H Hill / Sergey V Melnikov /
Abstract: Ribosome heterogeneity is a paradigm in biology, pertaining to the existence of structurally distinct populations of ribosomes within a single organism or cell. This concept suggests that ...Ribosome heterogeneity is a paradigm in biology, pertaining to the existence of structurally distinct populations of ribosomes within a single organism or cell. This concept suggests that structurally distinct pools of ribosomes have different functional properties and may be used to translate specific mRNAs. However, it is unknown to what extent structural heterogeneity reflects genuine functional specialization rather than stochastic variations in ribosome assembly. Here, we address this question by combining cryo-electron microscopy and tomography to observe individual structurally heterogeneous ribosomes in bacterial cells. We show that 70% of ribosomes in Psychrobacter urativorans contain a second copy of the ribosomal protein bS20 at a previously unknown binding site on the large ribosomal subunit. We then determine that this second bS20 copy appears to be functionally neutral. This demonstrates that ribosome heterogeneity does not necessarily lead to functional specialization, even when it involves significant variations such as the presence or absence of a ribosomal protein. Instead, we show that heterogeneous ribosomes can cooperate in general protein synthesis rather than specialize in translating discrete populations of mRNA.
History
DepositionFeb 17, 2025-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52842.png

Downloads & links

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Map

FileDownload / File: emd_52842.map.gz / Format: CCP4 / Size: 2.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRepresentative tomogram of cryo-FIB milled P. urativorans grown at physiological conditions
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.36 Å/pix.
x 450 pix.
= 4660.2 Å		10.36 Å/pix.
x 1440 pix.
= 14912.64 Å		10.36 Å/pix.
x 1024 pix.
= 10604.544 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.356 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-120.940820000000002 - 63.982235000000003
Average (Standard dev.)2.0427806 (±5.2811418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14401024450
Spacing10241440450
CellA: 10604.544 Å / B: 14912.64 Å / C: 4660.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tomogram of cryo-FIB milled Psychrobacter urativorans grown at ph...

EntireName: Tomogram of cryo-FIB milled Psychrobacter urativorans grown at physiological conditions
Components
  • Cell: Tomogram of cryo-FIB milled Psychrobacter urativorans grown at physiological conditions

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Supramolecule #1: Tomogram of cryo-FIB milled Psychrobacter urativorans grown at ph...

SupramoleculeName: Tomogram of cryo-FIB milled Psychrobacter urativorans grown at physiological conditions
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Psychrobacter urativorans (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 13 / Focused ion beam - Current: 0.01 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 92 K / Focused ion beam - Initial thickness: 2000 / Focused ion beam - Final thickness: 140
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos2. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 3.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 34

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