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Yorodumi- EMDB-14318: Cryo-EM reconstruction of the human 40S ribosomal subunit - Body ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14318 | |||||||||||||||
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Title | Cryo-EM reconstruction of the human 40S ribosomal subunit - Body domain | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Ribosome / rRNA modifications / post-translational modifications / cryo-EM | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.09 Å | |||||||||||||||
Authors | Pellegrino S / Dent KC / Spikes T / Warren AJ | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14318.map.gz | 37.5 MB | EMDB map data format | |
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Header (meta data) | emd-14318-v30.xml emd-14318.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14318_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_14318.png | 62.5 KB | ||
Filedesc metadata | emd-14318.cif.gz | 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14318 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14318 | HTTPS FTP |
-Validation report
Summary document | emd_14318_validation.pdf.gz | 404.5 KB | Display | EMDB validaton report |
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Full document | emd_14318_full_validation.pdf.gz | 404.1 KB | Display | |
Data in XML | emd_14318_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_14318_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14318 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14318 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14318.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8267 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Human 40S ribosomal subunit - Body domain
Entire | Name: Human 40S ribosomal subunit - Body domain |
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Components |
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-Supramolecule #1: Human 40S ribosomal subunit - Body domain
Supramolecule | Name: Human 40S ribosomal subunit - Body domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.56 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |