8P7Y
Mycoplasma pneumoniae 70S ribosome with second S4 protein on large subunit
This is a non-PDB format compatible entry.
Summary for 8P7Y
| Entry DOI | 10.2210/pdb8p7y/pdb |
| EMDB information | 17135 |
| Descriptor | 50S ribosomal protein L34, 30S ribosomal protein S2, 30S ribosomal protein S3, ... (67 entities in total) |
| Functional Keywords | in situ, ribosome, chloramphenicol, cryo-et, translation |
| Biological source | Mycoplasmoides pneumoniae M129 More |
| Total number of polymer chains | 59 |
| Total formula weight | 2393540.94 |
| Authors | Schacherl, M.,Xue, L.,Spahn, C.M.T.,Mahamid, J. (deposition date: 2023-05-31, release date: 2024-11-20, Last modification date: 2025-03-12) |
| Primary citation | Xue, L.,Spahn, C.M.T.,Schacherl, M.,Mahamid, J. Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells. Nat.Struct.Mol.Biol., 32:257-267, 2025 Cited by PubMed Abstract: Ribosome-targeting antibiotics represent an important class of antimicrobial drugs. Chloramphenicol (Cm) is a well-studied ribosomal peptidyl transferase center (PTC) binder and growing evidence suggests that its inhibitory action depends on the sequence of the nascent peptide. How such selective inhibition on the molecular scale manifests on the cellular level remains unclear. Here, we use cryo-electron tomography to analyze the impact of Cm inside the bacterium Mycoplasma pneumoniae. By resolving the Cm-bound ribosomes to 3.0 Å, we elucidate Cm's coordination with natural nascent peptides and transfer RNAs in the PTC. We find that Cm leads to the accumulation of a number of translation elongation states, indicating ongoing futile accommodation cycles, and to extensive ribosome collisions. We, thus, suggest that, beyond its direct inhibition of protein synthesis, the action of Cm may involve the activation of cellular stress responses. This work exemplifies how in-cell structural biology can expand the understanding of mechanisms of action for extensively studied antibiotics. PubMed: 39668257DOI: 10.1038/s41594-024-01441-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.7 Å) |
Structure validation
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