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Open data
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Basic information
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Title | Dibekacin-bound E.coli 70S ribosome in the PURE system | |||||||||
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![]() | RIBOSOME | |||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / 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 translational initiation / 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 / 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 / translational initiation / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.43 Å | |||||||||
![]() | Tomono J / Asano K / Chiashi T / Tanaka Y / Yokoyama T | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. Authors: Junta Tomono / Kosuke Asano / Takuma Chiashi / Masato Suzuki / Masayuki Igarashi / Yoshiaki Takahashi / Yoshikazu Tanaka / Takeshi Yokoyama / ![]() Abstract: The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to ...The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to visualize antibiotic actions on translating ribosomes in the cell-free system under macromolecular crowding conditions by cryo-electron microscopy, designated as the DARC method: the Direct visualization of Antibiotic binding on Ribosomes in the Cell-free translation system. This new method allows for acquiring a more comprehensive understanding of the mode of action of antibiotics on the translation inhibition without ribosome purification. Furthermore, with the direct link to biochemical analysis at the same condition as cryo-EM observation, we revealed the evolution of 2-DOS aminoglycosides from dibekacin (DBK) to arbekacin (ABK) by acquiring the synthetic tailored anchoring motif to lead to stronger binding affinity to ribosomes. Our cryo-EM structures of DBK and ABK bound ribosomes in the cell-free environment clearly depicted a synthetic tailored γ-amino-α-hydroxybutyryl (HABA) motif formed additional interactions with the ribosome enhancing antibiotic bindings. This new approach would be valuable for understanding the function of antibiotics for more efficient drug development. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 479.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 72.4 KB 72.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 112.2 KB | ||
Filedesc metadata | ![]() | 14.8 KB | ||
Others | ![]() ![]() | 410 MB 410 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ifbMC ![]() 8ifcC ![]() 8ifdC ![]() 8ifeC M: atomic model generated by this map C: citing same article ( |
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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: 0.788 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35411_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_35411_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : DBK-bound E.coli 70S ribosome in the PURE system
+Supramolecule #1: DBK-bound E.coli 70S ribosome in the PURE system
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #22: 23S ribosomal RNA
+Macromolecule #23: 5S ribosomal RNA
+Macromolecule #53: A-site tRNA-Phe
+Macromolecule #54: P-site tRNA-fMet
+Macromolecule #55: mRNA
+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, fully modified isoform
+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 L9
+Macromolecule #30: 50S ribosomal protein L13
+Macromolecule #31: 50S ribosomal protein L14
+Macromolecule #32: 50S ribosomal protein L15
+Macromolecule #33: 50S ribosomal protein L16
+Macromolecule #34: 50S ribosomal protein L17
+Macromolecule #35: 50S ribosomal protein L18
+Macromolecule #36: 50S ribosomal protein L19
+Macromolecule #37: 50S ribosomal protein L20
+Macromolecule #38: 50S ribosomal protein L21
+Macromolecule #39: 50S ribosomal protein L22
+Macromolecule #40: 50S ribosomal protein L23
+Macromolecule #41: 50S ribosomal protein L24
+Macromolecule #42: 50S ribosomal protein L25
+Macromolecule #43: 50S ribosomal protein L27
+Macromolecule #44: 50S ribosomal protein L28
+Macromolecule #45: 50S ribosomal protein L29
+Macromolecule #46: 50S ribosomal protein L30
+Macromolecule #47: 50S ribosomal protein L32
+Macromolecule #48: 50S ribosomal protein L33
+Macromolecule #49: 50S ribosomal protein L34
+Macromolecule #50: 50S ribosomal protein L35
+Macromolecule #51: 50S ribosomal protein L36
+Macromolecule #52: 50S ribosomal protein L31
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: SPERMIDINE
+Macromolecule #58: Dibekacin
+Macromolecule #59: SPERMINE
+Macromolecule #60: ZINC ION
-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: 7.6 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Details: covered with a homemade ultra-thin carbon film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 7775 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |