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- EMDB-10656: E. coli 70S ribosome in complex with dirithromycin, and deacylate... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10656 | ||||||||||||||||||
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Title | E. coli 70S ribosome in complex with dirithromycin, and deacylated tRNA(iMet) (focused classification). | ||||||||||||||||||
![]() | 70S ribosome in complex with dirithromycin and deacylated tRNAiMet in the P site | ||||||||||||||||||
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![]() | 70S ribosome / dirithromycin / antibiotics / cryo-EM / RIBOSOME | ||||||||||||||||||
Function / homology | ![]() stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / 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 / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 Å | ||||||||||||||||||
![]() | Pichkur EB / Polikanov YS | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the 70S ribosome. Authors: Evgeny B Pichkur / Alena Paleskava / Andrey G Tereshchenkov / Pavel Kasatsky / Ekaterina S Komarova / Dmitrii I Shiriaev / Alexey A Bogdanov / Olga A Dontsova / Ilya A Osterman / Petr V ...Authors: Evgeny B Pichkur / Alena Paleskava / Andrey G Tereshchenkov / Pavel Kasatsky / Ekaterina S Komarova / Dmitrii I Shiriaev / Alexey A Bogdanov / Olga A Dontsova / Ilya A Osterman / Petr V Sergiev / Yury S Polikanov / Alexander G Myasnikov / Andrey L Konevega / ![]() ![]() ![]() Abstract: Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and ...Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and interfering with protein synthesis. Dirithromycin is a derivative of the prototype macrolide erythromycin with additional hydrophobic side chain. In our recent study, we have discovered that the side chain of dirithromycin forms lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4 of the 70S ribosome. In the current work, we found that neither the presence of the side chain, nor the additional contact with the ribosome, improve the binding affinity of dirithromycin to the ribosome. Nevertheless, we found that dirithromycin is a more potent inhibitor of in vitro protein synthesis in comparison with its parent compound, erythromycin. Using high-resolution cryo-electron microscopy, we determined the structure of the dirithromycin bound to the translating 70S ribosome, which suggests that the better inhibitory properties of the drug could be rationalized by the side chain of dirithromycin pointing into the lumen of the nascent peptide exit tunnel, where it can interfere with the normal passage of the growing polypeptide chain. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 467.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 70.3 KB 70.3 KB | Display Display | ![]() |
Images | ![]() | 285.1 KB | ||
Filedesc metadata | ![]() | 14.4 KB | ||
Others | ![]() | 466.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xzaMC ![]() 6xz7C ![]() 6xzbC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 70S ribosome in complex with dirithromycin and deacylated tRNAiMet in the P site | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 70S ribosome in complex with dirithromycin and deacylated...
File | emd_10656_additional_1.map | ||||||||||||
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Annotation | 70S ribosome in complex with dirithromycin and deacylated tRNAiMet in the P site. Sharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : E. coli 70S ribosome in complex with dirithromycin and deacylated...
+Supramolecule #1: E. coli 70S ribosome in complex with dirithromycin and deacylated...
+Macromolecule #1: 16S rRNA
+Macromolecule #22: 23S rRNA
+Macromolecule #23: 5S rRNA
+Macromolecule #53: Deacylated tRNAi(Met)
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #24: 50S ribosomal protein L2
+Macromolecule #25: 50S ribosomal protein L3
+Macromolecule #26: 50S ribosomal protein L4
+Macromolecule #27: 50S ribosomal protein L5
+Macromolecule #28: 50S ribosomal protein L6
+Macromolecule #29: 50S ribosomal protein L10
+Macromolecule #30: 50S ribosomal protein L11
+Macromolecule #31: 50S ribosomal protein L13
+Macromolecule #32: 50S ribosomal protein L14
+Macromolecule #33: 50S ribosomal protein L15
+Macromolecule #34: 50S ribosomal protein L16
+Macromolecule #35: 50S ribosomal protein L17
+Macromolecule #36: 50S ribosomal protein L18
+Macromolecule #37: 50S ribosomal protein L19
+Macromolecule #38: 50S ribosomal protein L20
+Macromolecule #39: 50S ribosomal protein L21
+Macromolecule #40: 50S ribosomal protein L22
+Macromolecule #41: 50S ribosomal protein L23
+Macromolecule #42: 50S ribosomal protein L24
+Macromolecule #43: 50S ribosomal protein L25
+Macromolecule #44: 50S ribosomal protein L27
+Macromolecule #45: 50S ribosomal protein L28
+Macromolecule #46: 50S ribosomal protein L29
+Macromolecule #47: 50S ribosomal protein L30
+Macromolecule #48: 50S ribosomal protein L32
+Macromolecule #49: 50S ribosomal protein L33
+Macromolecule #50: 50S ribosomal protein L34
+Macromolecule #51: 50S ribosomal protein L35
+Macromolecule #52: 50S ribosomal protein L36
+Macromolecule #54: Dirithromycin
-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 |
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Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 2-27 / Average exposure time: 1.4 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.3 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 75000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |