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Yorodumi- EMDB-22632: Structure of the Bacterial Ribosome at 2 Angstrom Resolution (30S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22632 | |||||||||
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Title | Structure of the Bacterial Ribosome at 2 Angstrom Resolution (30S focused refinement) | |||||||||
Map data | 30S focused refined map | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.04 Å | |||||||||
Authors | Watson ZL / Ward FR / Meheust R / Ad O / Schepartz A / Banfield JF / Cate JHD | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2020 Title: Structure of the bacterial ribosome at 2 Å resolution. Authors: Zoe L Watson / Fred R Ward / Raphaël Méheust / Omer Ad / Alanna Schepartz / Jillian F Banfield / Jamie Hd Cate / Abstract: Using cryo-electron microscopy (cryo-EM), we determined the structure of the 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, ...Using cryo-electron microscopy (cryo-EM), we determined the structure of the 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22632.map.gz | 436 MB | EMDB map data format | |
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Header (meta data) | emd-22632-v30.xml emd-22632.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22632_fsc.xml | 17.5 KB | Display | FSC data file |
Images | emd_22632.png | 75.3 KB | ||
Others | emd_22632_half_map_1.map.gz emd_22632_half_map_2.map.gz | 373.6 MB 373.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22632 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22632 | HTTPS FTP |
-Validation report
Summary document | emd_22632_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_22632_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_22632_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22632 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22632 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22632.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 30S focused refined map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.7118 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: 30S focused refined half map 1
File | emd_22632_half_map_1.map | ||||||||||||
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Annotation | 30S focused refined half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 30S focused refined half map 2
File | emd_22632_half_map_2.map | ||||||||||||
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Annotation | 30S focused refined half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E. coli 70S ribosome
Entire | Name: E. coli 70S ribosome |
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Components |
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-Supramolecule #1: E. coli 70S ribosome
Supramolecule | Name: E. coli 70S ribosome / type: complex / ID: 1 / Parent: 0 Details: E. coli 70S ribosome bound to mRNA, tRNAs, and paromomycin |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
Molecular weight | Theoretical: 2.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.27 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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