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Open data
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Basic information
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Title | Streptomycin and Hygromycin B bound to the 30S body | ||||||||||||
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![]() | Antibiotic / RIBOSOME | ||||||||||||
Function / homology | ![]() ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / DNA endonuclease activity ...ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.08 Å | ||||||||||||
![]() | Paternoga H / Crowe-McAuliffe C / Novacek J / 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 | ![]() | 32.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 39.4 KB 39.4 KB | Display Display | ![]() |
Images | ![]() | 101.6 KB | ||
Filedesc metadata | ![]() | 9.4 KB | ||
Others | ![]() ![]() ![]() | 406 MB 410.5 MB 410.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8caiMC ![]() 8ca7C ![]() 8camC ![]() 8cazC ![]() 8cepC ![]() 8ceuC ![]() 8cf1C ![]() 8cf8C ![]() 8cgdC ![]() 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: 0.762 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
File | emd_16526_half_map_2.map | ||||||||||||
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Sample components
+Entire : 70S ribosomes with antibiotic cocktail
+Supramolecule #1: 70S ribosomes with antibiotic cocktail
+Macromolecule #1: 16S rRNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: Small ribosomal subunit protein uS3
+Macromolecule #4: Small ribosomal subunit protein uS4
+Macromolecule #5: Small ribosomal subunit protein uS5
+Macromolecule #6: Small ribosomal subunit protein bS6, non-modified isoform
+Macromolecule #7: Small ribosomal subunit protein uS8
+Macromolecule #8: Small ribosomal subunit protein uS11
+Macromolecule #9: Small ribosomal subunit protein uS12
+Macromolecule #10: Small ribosomal subunit protein uS15
+Macromolecule #11: 30S ribosomal protein S16
+Macromolecule #12: Small ribosomal subunit protein uS17
+Macromolecule #13: Small ribosomal subunit protein bS18
+Macromolecule #14: 30S ribosomal protein S20
+Macromolecule #15: Small ribosomal subunit protein bS21
+Macromolecule #16: POTASSIUM ION
+Macromolecule #17: HYGROMYCIN B VARIANT
+Macromolecule #18: [(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[...
+Macromolecule #19: SPECTINOMYCIN
+Macromolecule #20: MAGNESIUM ION
+Macromolecule #21: 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: 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 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: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 514855 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |