[English] 日本語
Yorodumi- PDB-7qq3: Cryo-EM structure of the E.coli 50S ribosomal subunit in complex ... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 7qq3 | |||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A. | |||||||||||||||||||||||||||||||||||||||||||||||||||
Components |
| |||||||||||||||||||||||||||||||||||||||||||||||||||
Keywords | RIBOSOME / Antibiotic / Myxovalargin A / MyxA | |||||||||||||||||||||||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationtranscriptional 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 / assembly of large subunit precursor of preribosome ...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 / assembly of large subunit precursor of preribosome / ribosome assembly / 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 / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / 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 | ![]() Myxococcus fulvus (bacteria) | |||||||||||||||||||||||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||
Authors | Koller, T.O. / Beckert, B. / Wilson, D.N. | |||||||||||||||||||||||||||||||||||||||||||||||||||
| Funding support | Germany, 1items
| |||||||||||||||||||||||||||||||||||||||||||||||||||
Citation | Journal: J Am Chem Soc / Year: 2023Title: 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
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 7qq3.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb7qq3.ent.gz | 1.5 MB | Display | PDB format |
| PDBx/mmJSON format | 7qq3.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7qq3_validation.pdf.gz | 528.3 KB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 7qq3_full_validation.pdf.gz | 595.3 KB | Display | |
| Data in XML | 7qq3_validation.xml.gz | 86.5 KB | Display | |
| Data in CIF | 7qq3_validation.cif.gz | 154 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qq3 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qq3 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 14121MC ![]() 8b7yC M: map data used to model this data C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
-
Assembly
| Deposited unit | ![]()
|
|---|---|
| 1 |
|
-
Components
-RNA chain , 2 types, 2 molecules IJ
| #1: RNA chain | Mass: 941752.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
|---|---|
| #2: RNA chain | Mass: 38815.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+50S ribosomal protein ... , 26 types, 26 molecules KLMORSTUVWXYZabcdefghijklm
-Protein/peptide , 1 types, 1 molecules B
| #29: Protein/peptide | Type: Peptide-like / Class: Antibiotic / Mass: 1678.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Myxococcus fulvus (bacteria) / References: BIRD: PRD_002442 |
|---|
-Non-polymers , 3 types, 174 molecules 




| #30: Chemical | ChemComp-MG / #31: Chemical | ChemComp-ZN / | #32: Water | ChemComp-HOH / | |
|---|
-Details
| Compound details | PubChem CID 137628402 |
|---|---|
| Has ligand of interest | Y |
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
|---|---|
| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
| Component | Name: Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A. Type: RIBOSOME / Entity ID: #1-#29 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Molecular weight | Value: 1.356 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
| Source (natural) | Organism: ![]() | |||||||||||||||||||||||||||||||||||
| Buffer solution | pH: 7.5 Details: Solutions were made fresh, pH was adjusted with potassium hydroxide at 4 degrees celcius and sterile filtered. | |||||||||||||||||||||||||||||||||||
| Buffer component |
| |||||||||||||||||||||||||||||||||||
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 7 OD(A260/mL) were applied to the grid. | |||||||||||||||||||||||||||||||||||
| Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R3/3 | |||||||||||||||||||||||||||||||||||
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 2 seconds blotting before plunging. |
-
Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
|---|---|
| Microscopy | Model: FEI TITAN KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Electron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
| Image scans | Movie frames/image: 40 |
-
Processing
| EM software |
| ||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 680054 | ||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 580425 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
| Atomic model building | Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||
| Atomic model building | PDB-ID: 4YBB Accession code: 4YBB / Source name: PDB / Type: experimental model |
Movie
Controller
About Yorodumi





Germany, 1items
Citation




PDBj































FIELD EMISSION GUN
