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- EMDB-52351: subtomogram average of the P. urativorans 70S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-52351
Titlesubtomogram average of the P. urativorans 70S ribosome
Map datasubtomogram average of the P. urativorans 70S ribosome
Sample
  • Complex: subtomogram average of the P. urativorans 70S ribosome
Keywordsribosome / S20 / bS20 / 70S / psychrobacter urativorans / psychrobacter / bacterial ribosome / cryo-ET / subtomogram average / in situ / in vivo
Biological speciesPsychrobacter urativorans (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 7.8 Å
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
DepositionDec 17, 2024-
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_52351.png

Downloads & links

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Map

FileDownload / File: emd_52351.map.gz / Format: CCP4 / Size: 47.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of the P. urativorans 70S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.59 Å/pix.
x 232 pix.
= 600.648 Å		2.59 Å/pix.
x 232 pix.
= 600.648 Å		2.59 Å/pix.
x 232 pix.
= 600.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.589 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00295
Minimum - Maximum-0.0027549153 - 0.011211633
Average (Standard dev.)0.000023397011 (±0.0005958492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions232232232
Spacing232232232
CellA=B=C: 600.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: subtomogram average of the P. urativorans 70S ribosome (half2)

Fileemd_52351_half_map_1.map
Annotationsubtomogram average of the P. urativorans 70S ribosome (half2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: subtomogram average of the P. urativorans 70S ribosome (half1)

Fileemd_52351_half_map_2.map
Annotationsubtomogram average of the P. urativorans 70S ribosome (half1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : subtomogram average of the P. urativorans 70S ribosome

EntireName: subtomogram average of the P. urativorans 70S ribosome
Components
  • Complex: subtomogram average of the P. urativorans 70S ribosome

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Supramolecule #1: subtomogram average of the P. urativorans 70S ribosome

SupramoleculeName: subtomogram average of the P. urativorans 70S ribosome
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Psychrobacter urativorans (bacteria)

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 37689
ExtractionNumber tomograms: 28 / Number images used: 60157
Final angle assignmentType: MAXIMUM LIKELIHOOD

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