8IFC
Arbekacin-bound E.coli 70S ribosome in the PURE system
This is a non-PDB format compatible entry.
Summary for 8IFC
| Entry DOI | 10.2210/pdb8ifc/pdb |
| EMDB information | 35412 |
| Descriptor | 16S ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (60 entities in total) |
| Functional Keywords | ribosome |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 55 |
| Total formula weight | 2212456.42 |
| Authors | Tomono, J.,Asano, K.,Chiashi, T.,Tanaka, Y.,Yokoyama, T. (deposition date: 2023-02-17, release date: 2024-02-14, Last modification date: 2024-06-19) |
| Primary citation | Tomono, J.,Asano, K.,Chiashi, T.,Suzuki, M.,Igarashi, M.,Takahashi, Y.,Tanaka, Y.,Yokoyama, T. Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. J.Biochem., 175:587-598, 2024 Cited by PubMed 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 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. PubMed: 38227611DOI: 10.1093/jb/mvae002 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.9 Å) |
Structure validation
Download full validation report
