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- EMDB-34986: Structure of 30S ribosomal subunit at 10 mM Magnesium concentration -

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Basic information

Entry
Database: EMDB / ID: EMD-34986
TitleStructure of 30S ribosomal subunit at 10 mM Magnesium concentration
Map data
Sample
  • Complex: Ribosomal 30S subunit
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsYu T / Zeng F
Funding support China, 3 items
OrganizationGrant numberCountry
Other government2021A1515010805 China
National Natural Science Foundation of China (NSFC)32171200 China
Other governmentJCYJ20220530115210023 China
CitationJournal: Biomolecules / Year: 2023
Title: Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations.
Authors: Ting Yu / Junyi Jiang / Qianxi Yu / Xin Li / Fuxing Zeng /
Abstract: Magnesium ions are abundant and play indispensable functions in the ribosome. A decrease in Mg concentration causes 70S ribosome dissociation and subsequent unfolding. Structural distortion at low Mg ...Magnesium ions are abundant and play indispensable functions in the ribosome. A decrease in Mg concentration causes 70S ribosome dissociation and subsequent unfolding. Structural distortion at low Mg concentrations has been observed in an immature pre50S, while the structural changes in mature subunits have not yet been studied. Here, we purified the 30S subunits of cells under various Mg concentrations and analyzed their structural distortion by cryo-electron microscopy. Upon systematically interrogating the structural heterogeneity within the 1 mM Mg dataset, we observed 30S particles with different levels of structural distortion in the decoding center, h17, and the 30S head. Our model showed that, when the Mg concentration decreases, the decoding center distorts, starting from h44 and followed by the shifting of h18 and h27, as well as the dissociation of ribosomal protein S12. Mg deficiency also eliminates the interactions between h17, h10, h15, and S16, resulting in the movement of h17 towards the tip of h6. More flexible structures were observed in the 30S head and platform, showing high variability in these regions. In summary, the structures resolved here showed several prominent distortion events in the decoding center and h17. The requirement for Mg in ribosomes suggests that the conformational changes reported here are likely shared due to a lack of cellular Mg in all domains of life.
History
DepositionDec 17, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34986.png

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Map

FileDownload / File: emd_34986.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.019728102 - 0.04033292
Average (Standard dev.)-1.3284385e-06 (±0.0010228794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34986_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_34986_half_map_2.map
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Sample components

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Entire : Ribosomal 30S subunit

EntireName: Ribosomal 30S subunit
Components
  • Complex: Ribosomal 30S subunit

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Supramolecule #1: Ribosomal 30S subunit

SupramoleculeName: Ribosomal 30S subunit / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Details: Ribosomal small subunit purified at 10 mM magnesium concentration
Source (natural)Organism: Escherichia coli (E. coli)

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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
Details: 20 mM HEPES-KOH pH7.5, 150 mM NH4Cl, 4 mM beta-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7k00

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192578
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

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