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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Clindamycin bound to the 50S subunit | ||||||||||||
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![]() | Antibiotic / RIBOSOME | ||||||||||||
Function / homology | ![]() transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.98 Å | ||||||||||||
![]() | Paternoga H / Koller TO / Beckert B / Wilson DN | ||||||||||||
Funding support | European Union, 3 items
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![]() | ![]() 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. | ||||||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 60.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 55 KB 55 KB | Display Display | ![]() |
Images | ![]() | 75.1 KB | ||
Filedesc metadata | ![]() | 11.6 KB | ||
Others | ![]() ![]() ![]() | 666.9 MB 668 MB 668.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cgdMC ![]() 8ca7C ![]() 8caiC ![]() 8camC ![]() 8cazC ![]() 8cepC ![]() 8ceuC ![]() 8cf1C ![]() 8cf8C ![]() 8cgiC ![]() 8cgjC ![]() 8cgkC ![]() 8cgrC ![]() 8cguC ![]() 8cgvC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.768 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Sample components
+Entire : 70S ribosomes with antibiotic cocktail
+Supramolecule #1: 70S ribosomes with antibiotic cocktail
+Macromolecule #1: Large ribosomal subunit protein bL33
+Macromolecule #2: Large ribosomal subunit protein bL34
+Macromolecule #3: Large ribosomal subunit protein bL35
+Macromolecule #4: Large ribosomal subunit protein bL36A
+Macromolecule #7: Large ribosomal subunit protein uL2
+Macromolecule #8: Large ribosomal subunit protein uL3
+Macromolecule #9: Large ribosomal subunit protein uL4
+Macromolecule #10: Large ribosomal subunit protein uL5
+Macromolecule #11: Large ribosomal subunit protein uL6
+Macromolecule #12: Large ribosomal subunit protein bL9
+Macromolecule #13: Large ribosomal subunit protein uL13
+Macromolecule #14: Large ribosomal subunit protein uL14
+Macromolecule #15: 50S ribosomal protein L15
+Macromolecule #16: Large ribosomal subunit protein uL16
+Macromolecule #17: Large ribosomal subunit protein bL17
+Macromolecule #18: Large ribosomal subunit protein uL18
+Macromolecule #19: Large ribosomal subunit protein bL19
+Macromolecule #20: Large ribosomal subunit protein bL20
+Macromolecule #21: Large ribosomal subunit protein bL21
+Macromolecule #22: Large ribosomal subunit protein uL22
+Macromolecule #23: Large ribosomal subunit protein uL23
+Macromolecule #24: Large ribosomal subunit protein uL24
+Macromolecule #25: 50S ribosomal protein L25
+Macromolecule #26: Large ribosomal subunit protein bL27
+Macromolecule #27: Large ribosomal subunit protein bL28
+Macromolecule #28: Large ribosomal subunit protein uL29
+Macromolecule #29: Large ribosomal subunit protein uL30
+Macromolecule #30: Large ribosomal subunit protein bL32
+Macromolecule #5: 23S rRNA
+Macromolecule #6: 5S rRNA
+Macromolecule #31: ZINC ION
+Macromolecule #32: ACETATE ION
+Macromolecule #33: CLINDAMYCIN
+Macromolecule #34: APRAMYCIN
+Macromolecule #35: MAGNESIUM ION
+Macromolecule #36: POTASSIUM ION
+Macromolecule #37: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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) / Detector mode: COUNTING / Average exposure time: 4.5 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 275137 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |