+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15712 | ||||||||||||||||||||||||
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Title | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | ||||||||||||||||||||||||
Map data | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | ||||||||||||||||||||||||
Sample |
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Keywords | Antibiotic / Initiator tRNA / Complex / Macromolecule / RIBOSOME | ||||||||||||||||||||||||
Function / homology | Function and homology information 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 DNA-templated DNA replication initiation / negative regulation of translational 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 / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / 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 / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.96 Å | ||||||||||||||||||||||||
Authors | Sanyal S / Parajuli NP / Emmerich AG | ||||||||||||||||||||||||
Funding support | Sweden, United States, 7 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria. Authors: Narayan Prasad Parajuli / Andrew Emmerich / Chandra Sekhar Mandava / Michael Y Pavlov / Suparna Sanyal / Abstract: Thermorubin (THB) is a long-known broad-spectrum ribosome-targeting antibiotic, but the molecular mechanism of its action was unclear. Here, our precise fast-kinetics assays in a reconstituted ...Thermorubin (THB) is a long-known broad-spectrum ribosome-targeting antibiotic, but the molecular mechanism of its action was unclear. Here, our precise fast-kinetics assays in a reconstituted Escherichia coli translation system and 1.96 Å resolution cryo-EM structure of THB-bound 70S ribosome with mRNA and initiator tRNA, independently suggest that THB binding at the intersubunit bridge B2a near decoding center of the ribosome interferes with the binding of A-site substrates aminoacyl-tRNAs and class-I release factors, thereby inhibiting elongation and termination steps of bacterial translation. Furthermore, THB acts as an anti-dissociation agent that tethers the ribosomal subunits and blocks ribosome recycling, subsequently reducing the pool of active ribosomes. Our results show that THB does not inhibit translation initiation as proposed earlier and provide a complete mechanism of how THB perturbs bacterial protein synthesis. This in-depth characterization will hopefully spur efforts toward the design of THB analogs with improved solubility and effectivity against multidrug-resistant bacteria. | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15712.map.gz | 484.1 MB | EMDB map data format | |
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Header (meta data) | emd-15712-v30.xml emd-15712.xml | 71.2 KB 71.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15712_fsc.xml | 16.7 KB | Display | FSC data file |
Images | emd_15712.png | 167.1 KB | ||
Filedesc metadata | emd-15712.cif.gz | 13.7 KB | ||
Others | emd_15712_half_map_1.map.gz emd_15712_half_map_2.map.gz | 475 MB 475 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15712 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15712 | HTTPS FTP |
-Validation report
Summary document | emd_15712_validation.pdf.gz | 880.3 KB | Display | EMDB validaton report |
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Full document | emd_15712_full_validation.pdf.gz | 879.8 KB | Display | |
Data in XML | emd_15712_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_15712_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15712 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15712 | HTTPS FTP |
-Related structure data
Related structure data | 8ayeMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15712.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: E. coli 70S ribosome bound to thermorubin and fMet-tRNA
File | emd_15712_half_map_1.map | ||||||||||||
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Annotation | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: E. coli 70S ribosome bound to thermorubin and fMet-tRNA
File | emd_15712_half_map_2.map | ||||||||||||
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Annotation | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : E. coli 70S ribosome bound to thermorubin and fMet-tRNA
+Supramolecule #1: E. coli 70S ribosome bound to thermorubin and fMet-tRNA
+Macromolecule #1: 50S ribosomal protein L33
+Macromolecule #2: 50S ribosomal protein L34
+Macromolecule #3: 50S ribosomal protein L35
+Macromolecule #4: 50S ribosomal protein L36
+Macromolecule #5: 50S ribosomal protein L31
+Macromolecule #8: 30S ribosomal protein S2
+Macromolecule #9: 30S ribosomal protein S3
+Macromolecule #10: 30S ribosomal protein S4
+Macromolecule #11: 30S ribosomal protein S5
+Macromolecule #12: 30S ribosomal protein S6, fully modified isoform
+Macromolecule #13: 30S ribosomal protein S7
+Macromolecule #14: 30S ribosomal protein S8
+Macromolecule #15: 30S ribosomal protein S9
+Macromolecule #16: 30S ribosomal protein S10
+Macromolecule #17: 30S ribosomal protein S11
+Macromolecule #18: 30S ribosomal protein S12
+Macromolecule #19: 30S ribosomal protein S13
+Macromolecule #20: 30S ribosomal protein S14
+Macromolecule #21: 30S ribosomal protein S15
+Macromolecule #22: 30S ribosomal protein S16
+Macromolecule #23: 30S ribosomal protein S17
+Macromolecule #24: 30S ribosomal protein S18
+Macromolecule #25: 30S ribosomal protein S19
+Macromolecule #26: 30S ribosomal protein S20
+Macromolecule #27: 30S ribosomal protein S21
+Macromolecule #32: 50S ribosomal protein L2
+Macromolecule #33: 50S ribosomal protein L3
+Macromolecule #34: 50S ribosomal protein L4
+Macromolecule #35: 50S ribosomal protein L5
+Macromolecule #36: 50S ribosomal protein L6
+Macromolecule #37: 50S ribosomal protein L9
+Macromolecule #38: 50S ribosomal protein L13
+Macromolecule #39: 50S ribosomal protein L14
+Macromolecule #40: 50S ribosomal protein L15
+Macromolecule #41: 50S ribosomal protein L16
+Macromolecule #42: 50S ribosomal protein L17
+Macromolecule #43: 50S ribosomal protein L18
+Macromolecule #44: 50S ribosomal protein L19
+Macromolecule #45: 50S ribosomal protein L20
+Macromolecule #46: 50S ribosomal protein L21
+Macromolecule #47: 50S ribosomal protein L22
+Macromolecule #48: 50S ribosomal protein L23
+Macromolecule #49: 50S ribosomal protein L24
+Macromolecule #50: 50S ribosomal protein L25
+Macromolecule #51: 50S ribosomal protein L27
+Macromolecule #52: 50S ribosomal protein L28
+Macromolecule #53: 50S ribosomal protein L29
+Macromolecule #54: 50S ribosomal protein L30
+Macromolecule #55: 50S ribosomal protein L32
+Macromolecule #6: E-site tRNA
+Macromolecule #7: 16S rRNA
+Macromolecule #28: mRNA
+Macromolecule #29: P-site tRNA-fMet
+Macromolecule #30: 23S rRNA
+Macromolecule #31: 5S rRNA
+Macromolecule #56: ZINC ION
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: Thermorubin
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.745 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |