[English] 日本語
Yorodumi- EMDB-14121: Cryo-EM structure of the E.coli 50S ribosomal subunit in complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14121 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A. | |||||||||
Map data | Masked post processed map | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / 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 (E. coli) / Escherichia coli K-12 (bacteria) / Myxococcus fulvus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Koller TO / Beckert B / Wilson DN | |||||||||
Funding support | Germany, 1 items
| |||||||||
Citation | Journal: J Am Chem Soc / Year: 2023 Title: The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition. Authors: Timm O Koller / Ullrich Scheid / Teresa Kösel / Jennifer Herrmann / Daniel Krug / Helena I M Boshoff / Bertrand Beckert / Joanna C Evans / Jan Schlemmer / Becky Sloan / Danielle M Weiner / ...Authors: Timm O Koller / Ullrich Scheid / Teresa Kösel / Jennifer Herrmann / Daniel Krug / Helena I M Boshoff / Bertrand Beckert / Joanna C Evans / Jan Schlemmer / Becky Sloan / Danielle M Weiner / Laura E Via / Atica Moosa / Thomas R Ioerger / Michael Graf / Boris Zinshteyn / Maha Abdelshahid / Fabian Nguyen / Stefan Arenz / Franziska Gille / Maik Siebke / Tim Seedorf / Oliver Plettenburg / Rachel Green / Anna-Luisa Warnke / Joachim Ullrich / Ralf Warrass / Clifton E Barry / Digby F Warner / Valerie Mizrahi / Andreas Kirschning / Daniel N Wilson / Rolf Müller / Abstract: Resistance of bacterial pathogens against antibiotics is declared by WHO as a major global health threat. As novel antibacterial agents are urgently needed, we re-assessed the broad-spectrum ...Resistance of bacterial pathogens against antibiotics is declared by WHO as a major global health threat. As novel antibacterial agents are urgently needed, we re-assessed the broad-spectrum myxobacterial antibiotic myxovalargin and found it to be extremely potent against . To ensure compound supply for further development, we studied myxovalargin biosynthesis in detail enabling production via fermentation of a native producer. Feeding experiments as well as functional genomics analysis suggested a structural revision, which was eventually corroborated by the development of a concise total synthesis. The ribosome was identified as the molecular target based on resistant mutant sequencing, and a cryo-EM structure revealed that myxovalargin binds within and completely occludes the exit tunnel, consistent with a mode of action to arrest translation during a late stage of translation initiation. These studies open avenues for structure-based scaffold improvement toward development as an antibacterial agent. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_14121.map.gz | 23 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-14121-v30.xml emd-14121.xml | 52.1 KB 52.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14121_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_14121.png | 78.8 KB | ||
Others | emd_14121_additional_1.map.gz emd_14121_additional_2.map.gz emd_14121_half_map_1.map.gz emd_14121_half_map_2.map.gz | 166.4 MB 139.8 MB 140.5 MB 140.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14121 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14121 | HTTPS FTP |
-Validation report
Summary document | emd_14121_validation.pdf.gz | 783.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_14121_full_validation.pdf.gz | 783.3 KB | Display | |
Data in XML | emd_14121_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | emd_14121_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14121 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14121 | HTTPS FTP |
-Related structure data
Related structure data | 7qq3MC 8b7yC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_14121.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Masked post processed map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: post processed map
File | emd_14121_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | post processed map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: 3D refined map
File | emd_14121_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 3D refined map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_14121_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1
File | emd_14121_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Cryo-EM structure of the E.coli 50S ribosomal subunit in complex ...
+Supramolecule #1: Cryo-EM structure of the E.coli 50S ribosomal subunit in complex ...
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L6
+Macromolecule #7: 50S ribosomal protein L13
+Macromolecule #8: 50S ribosomal protein L14
+Macromolecule #9: 50S ribosomal protein L15
+Macromolecule #10: 50S ribosomal protein L16
+Macromolecule #11: 50S ribosomal protein L17
+Macromolecule #12: 50S ribosomal protein L18
+Macromolecule #13: 50S ribosomal protein L19
+Macromolecule #14: 50S ribosomal protein L20
+Macromolecule #15: 50S ribosomal protein L21
+Macromolecule #16: 50S ribosomal protein L22
+Macromolecule #17: 50S ribosomal protein L23
+Macromolecule #18: 50S ribosomal protein L24
+Macromolecule #19: 50S ribosomal protein L25
+Macromolecule #20: 50S ribosomal protein L27
+Macromolecule #21: 50S ribosomal protein L28
+Macromolecule #22: 50S ribosomal protein L29
+Macromolecule #23: 50S ribosomal protein L30
+Macromolecule #24: 50S ribosomal protein L32
+Macromolecule #25: 50S ribosomal protein L33
+Macromolecule #26: 50S ribosomal protein L34
+Macromolecule #27: 50S ribosomal protein L35
+Macromolecule #28: 50S ribosomal protein L36
+Macromolecule #29: Myxovalargin A
+Macromolecule #30: MAGNESIUM ION
+Macromolecule #31: ZINC ION
+Macromolecule #32: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: Solutions were made fresh, pH was adjusted with potassium hydroxide at 4 degrees celcius and sterile filtered. | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 300.0 nm | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 2 seconds blotting before plunging.. | |||||||||||||||||||||
Details | 7 OD(A260/mL) were applied to the grid. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |