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- EMDB-18814: The structure of the human 80S ribosome at 1.9 angstrom resolutio... -
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Open data
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Basic information
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Title | The 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 40S subunit head | |||||||||||||||
![]() | Focused refinement of the 40S ribosomal subunit head using the multibody job in relion. | |||||||||||||||
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![]() | ribosome / cryo-electron microscopie / post-transcriptional modifications | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.9 Å | |||||||||||||||
![]() | Holvec S / Barchet C / Frechin L / Hazemann I / von Loeffelholz O / Klaholz BP | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 11.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.3 KB 15.3 KB | Display Display | ![]() |
Images | ![]() | 19.8 KB | ||
Filedesc metadata | ![]() | 4.3 KB | ||
Others | ![]() ![]() | 186.5 MB 186.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 618.1 KB | Display | ![]() |
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Full document | ![]() | 617.7 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Focused refinement of the 40S ribosomal subunit head using the multibody job in relion. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: First half-map of the 40S subunit head map.
File | emd_18814_half_map_1.map | ||||||||||||
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Annotation | First half-map of the 40S subunit head map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half-map of the 40S subunit head map.
File | emd_18814_half_map_2.map | ||||||||||||
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Annotation | Second half-map of the 40S subunit head map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human 60S ribosomal subunit
Entire | Name: Human 60S ribosomal subunit |
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Components |
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-Supramolecule #1: Human 60S ribosomal subunit
Supramolecule | Name: Human 60S ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.6 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV |
Details | Purified from HeLa cells. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.1 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen 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 model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 382016 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |