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- EMDB-18812: The structure of the human 80S ribosome at 1.9 angstrom resolutio... -

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Entry
Database: EMDB / ID: EMD-18812
TitleThe structure of the human 80S ribosome at 1.9 angstrom resolution reveals the molecular role of chemical modifications and ions in RNA - Focused refinement of the of the 60S subunit
Map dataFocused refinement of the 60S ribosome subunit using the multibody job in relion.
Sample
  • Complex: Human 60S ribosomal subunit
Keywordsribosome / cryo-electron microscopie / post-transcriptional modifications
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsHolvec S / Barchet C / Frechin L / Hazemann I / von Loeffelholz O / Klaholz BP
Funding support France, 4 items
OrganizationGrant numberCountry
Fondation ARC France
Agence Nationale de la Recherche (ANR) France
Fondation pour la Recherche Medicale (FRM) France
La ligue contre le cancer France
Citation
Journal: Nat Struct Mol Biol / Year: 2024
Title: The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA.
Authors: Samuel Holvec / Charles Barchet / Antony Lechner / Léo Fréchin / S Nimali T De Silva / Isabelle Hazemann / Philippe Wolff / Ottilie von Loeffelholz / Bruno P Klaholz /
Abstract: The ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. Here we present the 1.9 Å resolution cryo ...The ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. Here we present the 1.9 Å resolution cryo electron microscopy structure of the 80S human ribosome resolving numerous new ribosomal RNA modifications and functionally important ions such as Zn, K and Mg, including their associated individual water molecules. The 2'-O-methylation, pseudo-uridine and base modifications were confirmed by mass spectrometry, resulting in a complete investigation of the >230 sites, many of which could not be addressed previously. They choreograph key interactions within the RNA and at the interface with proteins, including at the ribosomal subunit interfaces of the fully assembled 80S ribosome. Uridine isomerization turns out to be a key mechanism for U-A base pair stabilization in RNA in general. The structural environment of chemical modifications and ions is primordial for the RNA architecture of the mature human ribosome, hence providing a structural framework to address their role in healthy states and in human diseases.
#1: Journal: Biorxiv / Year: 2023
Title: Structure of the human 80S ribosome at 1.9 angstrom resolution - the molecular role of chemical modifications and ions in RNA
Authors: Holvec S / Barchet C / Lechner A / Frechin L / Silva SNTD / Hazemann I / Wolff P / Loeffelholz OV / Klaholz BP
History
DepositionNov 2, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18812.png

Downloads & links

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Map

FileDownload / File: emd_18812.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement of the 60S ribosome subunit using the multibody job in relion.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.78 Å/pix.
x 64 pix.
= 241.92 Å		3.78 Å/pix.
x 64 pix.
= 241.92 Å		3.78 Å/pix.
x 64 pix.
= 241.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.0.820.820.82
CCP4 map header3.783.783.78
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0175
Minimum - Maximum-0.08331195 - 0.22245601
Average (Standard dev.)0.00033455843 (±0.0042102626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Second half-map of the 60S subunit map.

Fileemd_18812_half_map_1.map
AnnotationSecond half-map of the 60S subunit map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human 60S ribosomal subunit

EntireName: Human 60S ribosomal subunit
Components
  • Complex: Human 60S ribosomal subunit

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Supramolecule #1: Human 60S ribosomal subunit

SupramoleculeName: Human 60S ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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

Concentration1.0 mg/mL
BufferpH: 7.6
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified from HeLa cells.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6528 / Average exposure time: 3.58 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.1 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3883

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 382016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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