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Yorodumi- EMDB-10655: E. coli 50S ribosomal subunit in complex with dirithromycin, fMet... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10655 | ||||||||||||||||||
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Title | E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). | ||||||||||||||||||
Map data | Sharpened map of the 50S LSU with Dirithromycin after high-order aberration correction in Relion 3.1 | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / 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 / 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 / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / 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 | Escherichia coli (strain K12) (bacteria) / Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | ||||||||||||||||||
Authors | Pichkur EB / Polikanov YS / Myasnikov AG / Konevega AL | ||||||||||||||||||
Funding support | Russian Federation, United States, 5 items
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Citation | Journal: RNA / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10655.map.gz | 25.9 MB | EMDB map data format | |
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Header (meta data) | emd-10655-v30.xml emd-10655.xml | 57.2 KB 57.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10655_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_10655.png | 185.9 KB | ||
Masks | emd_10655_msk_1.map | 512 MB | Mask map | |
Others | emd_10655_additional.map.gz emd_10655_half_map_1.map.gz emd_10655_half_map_2.map.gz | 475.5 MB 412.7 MB 412.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10655 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10655 | HTTPS FTP |
-Validation report
Summary document | emd_10655_validation.pdf.gz | 411.5 KB | Display | EMDB validaton report |
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Full document | emd_10655_full_validation.pdf.gz | 410.7 KB | Display | |
Data in XML | emd_10655_validation.xml.gz | 23.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10655 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10655 | HTTPS FTP |
-Related structure data
Related structure data | 6xz7MC 6xzaC 6xzbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_10655.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map of the 50S LSU with Dirithromycin after high-order aberration correction in Relion 3.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_10655_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: A map calculated and sharpened in CisTEM before...
File | emd_10655_additional.map | ||||||||||||
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Annotation | A map calculated and sharpened in CisTEM before high-order aberrations correction in Relion 3.1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half #2
File | emd_10655_half_map_1.map | ||||||||||||
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Annotation | Half #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half #1
File | emd_10655_half_map_2.map | ||||||||||||
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Annotation | Half #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : E. coli 50S ribosomal subunit in complex with dirithromycin, fMet...
+Supramolecule #1: E. coli 50S ribosomal subunit in complex with dirithromycin, fMet...
+Supramolecule #2: E. coli 50S ribosomal subunit
+Supramolecule #3: fMet-Phe-tRNA(Phe)
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #32: Deacylated tRNAi(Met)
+Macromolecule #33: fMet-Phe-tRNA(Phe)
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L10
+Macromolecule #9: 50S ribosomal protein L11
+Macromolecule #10: 50S ribosomal protein L13
+Macromolecule #11: 50S ribosomal protein L14
+Macromolecule #12: 50S ribosomal protein L15
+Macromolecule #13: 50S ribosomal protein L16
+Macromolecule #14: 50S ribosomal protein L17
+Macromolecule #15: 50S ribosomal protein L18
+Macromolecule #16: 50S ribosomal protein L19
+Macromolecule #17: 50S ribosomal protein L20
+Macromolecule #18: 50S ribosomal protein L21
+Macromolecule #19: 50S ribosomal protein L22
+Macromolecule #20: 50S ribosomal protein L23
+Macromolecule #21: 50S ribosomal protein L24
+Macromolecule #22: 50S ribosomal protein L25
+Macromolecule #23: 50S ribosomal protein L27
+Macromolecule #24: 50S ribosomal protein L28
+Macromolecule #25: 50S ribosomal protein L29
+Macromolecule #26: 50S ribosomal protein L30
+Macromolecule #27: 50S ribosomal protein L32
+Macromolecule #28: 50S ribosomal protein L33
+Macromolecule #29: 50S ribosomal protein L34
+Macromolecule #30: 50S ribosomal protein L35
+Macromolecule #31: 50S ribosomal protein L36
+Macromolecule #34: MAGNESIUM ION
+Macromolecule #35: Dirithromycin
+Macromolecule #36: 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 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |