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Yorodumi- EMDB-16520: Omadacycline and spectinomycin bound to the 30S ribosomal subunit head -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16520 | ||||||||||||
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Title | Omadacycline and spectinomycin bound to the 30S ribosomal subunit head | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Ribosome / antibiotics / spectinomycin / omadacycline | ||||||||||||
Function / homology | Function and homology information transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / maintenance of translational fidelity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit ...transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / maintenance of translational fidelity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / RNA binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli BW25113 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.06 Å | ||||||||||||
Authors | Paternoga H / Crowe-McAuliffe C / Wilson DN | ||||||||||||
Funding support | European Union, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structural conservation of antibiotic interaction with ribosomes. Authors: Helge Paternoga / Caillan Crowe-McAuliffe / Lars V Bock / Timm O Koller / Martino Morici / Bertrand Beckert / Alexander G Myasnikov / Helmut Grubmüller / Jiří Nováček / Daniel N Wilson / Abstract: The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron- ...The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16520.map.gz | 26.6 MB | EMDB map data format | |
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Header (meta data) | emd-16520-v30.xml emd-16520.xml | 33.4 KB 33.4 KB | Display Display | EMDB header |
Images | emd_16520.png | 118.5 KB | ||
Others | emd_16520_additional_1.map.gz emd_16520_half_map_1.map.gz emd_16520_half_map_2.map.gz | 402.5 MB 408.7 MB 408.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16520 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16520 | HTTPS FTP |
-Related structure data
Related structure data | 8ca7MC 8caiC 8camC 8cazC 8cepC 8ceuC 8cf1C 8cf8C 8cgdC 8cgiC 8cgjC 8cgkC 8cgrC 8cguC 8cgvC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16520.map.gz / Format: CCP4 / Size: 512 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: 0.762 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Sharpened map
File | emd_16520_additional_1.map | ||||||||||||
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Annotation | Sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16520_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16520_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ribosomal small subunit head
+Supramolecule #1: Ribosomal small subunit head
+Macromolecule #1: 16S rRNA
+Macromolecule #2: Small ribosomal subunit protein uS3
+Macromolecule #3: Small ribosomal subunit protein uS5
+Macromolecule #4: 30S ribosomal protein S7
+Macromolecule #5: Small ribosomal subunit protein uS9
+Macromolecule #6: Small ribosomal subunit protein uS10
+Macromolecule #7: Small ribosomal subunit protein uS13
+Macromolecule #8: Small ribosomal subunit protein uS14
+Macromolecule #9: Small ribosomal subunit protein uS19
+Macromolecule #10: POTASSIUM ION
+Macromolecule #11: Omadacycline
+Macromolecule #12: SPECTINOMYCIN
+Macromolecule #13: MAGNESIUM ION
+Macromolecule #14: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 24195 / Average exposure time: 4.0 sec. / Average electron dose: 44.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 514855 |