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- EMDB-14319: Cryo-EM reconstruction of the human 40S ribosomal subunit - Head ... -

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Basic information

Entry
Database: EMDB / ID: EMD-14319
TitleCryo-EM reconstruction of the human 40S ribosomal subunit - Head domain
Map data
Sample
  • Complex: Human 40S ribosomal subunit
KeywordsRibosome / rRNA modifications / post-translational modifications / cryo-EM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsPellegrino S / Dent KC / Spikes T / Warren AJ
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Kay Kendall Leukaemia Fund United Kingdom
Bloodwise12048 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105161083 United Kingdom
Wellcome Trust100140 United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution.
Authors: Simone Pellegrino / Kyle C Dent / Tobias Spikes / Alan J Warren /
Abstract: The chemical modification of ribosomal RNA and proteins is critical for ribosome assembly, for protein synthesis and may drive ribosome specialisation in development and disease. However, the ...The chemical modification of ribosomal RNA and proteins is critical for ribosome assembly, for protein synthesis and may drive ribosome specialisation in development and disease. However, the inability to accurately visualise these modifications has limited mechanistic understanding of the role of these modifications in ribosome function. Here we report the 2.15 Å resolution cryo-EM reconstruction of the human 40S ribosomal subunit. We directly visualise post-transcriptional modifications within the 18S rRNA and four post-translational modifications of ribosomal proteins. Additionally, we interpret the solvation shells in the core regions of the 40S ribosomal subunit and reveal how potassium and magnesium ions establish both universally conserved and eukaryote-specific coordination to promote the stabilisation and folding of key ribosomal elements. This work provides unprecedented structural details for the human 40S ribosomal subunit that will serve as an important reference for unravelling the functional role of ribosomal RNA modifications.
History
DepositionFeb 9, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14319.png

Downloads & links

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Map

FileDownload / File: emd_14319.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 423.27 Å		0.83 Å/pix.
x 512 pix.
= 423.27 Å		0.83 Å/pix.
x 512 pix.
= 423.27 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.08534437 - 0.21093719
Average (Standard dev.)0.00009808525 (±0.0023638601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 423.2704 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human 40S ribosomal subunit

EntireName: Human 40S ribosomal subunit
Components
  • Complex: Human 40S ribosomal subunit

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Supramolecule #1: Human 40S ribosomal subunit

SupramoleculeName: Human 40S ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.56 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 546717
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 474276
FSC plot (resolution estimation)

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