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Open data
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Basic information
Entry | Database: PDB / ID: 8cgk | ||||||||||||
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Title | Lincomycin and Avilamycin bound to the 50S subunit | ||||||||||||
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![]() | RIBOSOME / Antibiotic | ||||||||||||
Function / homology | ![]() 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 / ribosomal large subunit 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 / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.64 Å | ||||||||||||
![]() | Paternoga, H. / Crowe-McAuliffe, C. / Beckert, B. / Wilson, D.N. | ||||||||||||
Funding support | European Union, 3items
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![]() | ![]() Title: Structural conservation of antibiotic interaction with ribosomes. Authors: Helge Paternoga / Caillan Crowe-McAuliffe / Lars V Bock / Timm O Koller / Martino Morici / Bertrand Beckert / Alexander G Myasnikov / Helmut Grubmüller / Jiří Nováček / Daniel N Wilson / ![]() ![]() ![]() Abstract: The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron- ...The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies. | ||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.3 MB | Display | ![]() |
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PDB format | ![]() | 1.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 16646MC ![]() 8ca7C ![]() 8caiC ![]() 8camC ![]() 8cazC ![]() 8cepC ![]() 8ceuC ![]() 8cf1C ![]() 8cf8C ![]() 8cgdC ![]() 8cgiC ![]() 8cgjC ![]() 8cgrC ![]() 8cguC ![]() 8cgvC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Assembly
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Components
+Large ribosomal subunit protein ... , 24 types, 24 molecules 0123cdeghijlmopqrstvwxyz
-RNA chain , 2 types, 2 molecules ab
#5: RNA chain | Mass: 941811.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-50S ribosomal protein ... , 2 types, 2 molecules ku
#14: Protein | Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#23: Protein | Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 7 types, 7446 molecules ![](data/chem/img/ZN.gif)
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#29: Chemical | ChemComp-ZN / |
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#30: Chemical | ChemComp-ACT / |
#31: Chemical | ChemComp-3QB / |
#32: Chemical | ChemComp-6UQ / ( |