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Yorodumi- EMDB-14052: Specific features and methylation sites of a plant ribosome. 80S ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14052 | |||||||||||||||
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Title | Specific features and methylation sites of a plant ribosome. 80S translating ribosome (A/P-P/E). | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Solanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA / RIBOSOME | |||||||||||||||
Biological species | Solanum lycopersicum (tomato) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||
Authors | Cottilli P / Itoh Y / Amunts A | |||||||||||||||
Funding support | European Union, 4 items
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Citation | Journal: Plant Commun / Year: 2022 Title: Cryo-EM structure and rRNA modification sites of a plant ribosome. Authors: Patrick Cottilli / Yuzuru Itoh / Yuko Nobe / Anton S Petrov / Purificación Lisón / Masato Taoka / Alexey Amunts / Abstract: Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to ...Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14052.map.gz | 332.6 MB | EMDB map data format | |
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Header (meta data) | emd-14052-v30.xml emd-14052.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14052_fsc.xml | 19.1 KB | Display | FSC data file |
Images | emd_14052.png | 100.1 KB | ||
Masks | emd_14052_msk_1.map | 600.7 MB | Mask map | |
Filedesc metadata | emd-14052.cif.gz | 3.9 KB | ||
Others | emd_14052_half_map_1.map.gz emd_14052_half_map_2.map.gz | 487.1 MB 487.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14052 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14052 | HTTPS FTP |
-Validation report
Summary document | emd_14052_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_14052_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_14052_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | emd_14052_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14052 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14052 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14052.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14052_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14052_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14052_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 80S translating ribosome (A/P-P/E)
Entire | Name: 80S translating ribosome (A/P-P/E) |
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Components |
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-Supramolecule #1: 80S translating ribosome (A/P-P/E)
Supramolecule | Name: 80S translating ribosome (A/P-P/E) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#45 |
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Source (natural) | Organism: Solanum lycopersicum (tomato) |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.2 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 |