8ZFF
Structure of the Bacterial Ribosome without hypoxia-induced rRNA modifications
This is a non-PDB format compatible entry.
Summary for 8ZFF
| Entry DOI | 10.2210/pdb8zff/pdb |
| EMDB information | 60059 |
| Descriptor | 16S rRNA, Small ribosomal subunit protein uS10, Small ribosomal subunit protein uS11, ... (55 entities in total) |
| Functional Keywords | rrna modifications, translation, ribosome |
| Biological source | Escherichia coli BW25113 More |
| Total number of polymer chains | 54 |
| Total formula weight | 2197672.58 |
| Authors | Ishiguro, K.,Yokoyama, T.,Shirouzu, M.,Ito, T.,Suzuki, T. (deposition date: 2024-05-07, release date: 2025-11-12, Last modification date: 2026-05-27) |
| Primary citation | Ishiguro, K.,Midorikawa, K.,Shigi, N.,Kimura, S.,Liiv, A.,Yokoyama, T.,Ito, T.,Shirouzu, M.,Remme, J.,Miyauchi, K.,Suzuki, T. Hypoxia-induced ribosomal RNA modifications in the peptidyl-transferase center contribute to anaerobic growth of bacteria. Mol.Cell, 86:78-96.e10, 2026 Cited by PubMed Abstract: Ribosomal RNAs (rRNAs) contain various modifications that play critical roles in ribosome assembly and function. Here, we discovered two stereoselective methylations of the rRNA backbone in the peptidyl-transferase center (PTC) of the 50S subunit of Escherichia coli cultured under anaerobic conditions. Methylation occurs at carbon 5'(S) of ribose moieties of dihydrouridine at position 2449 (Dm2449) and 2'-O-metylcytidine at position 2498 (Cmm2498). We identified the rlmX gene, encoding a cobalamin-dependent radical S-adenosylmethionine (SAM) methyltransferase responsible for these methylations. Intriguingly, Dm2449, Cmm2498, and 5-hydroxycytidine (hoC2501) in the PTC were elevated under anaerobic growth conditions. A double knockout strain lacking rlmX and rlhA (responsible for hoC2501) impaired anaerobic growth. Biochemical studies showed that these rRNA modifications stimulate protein synthesis. The cryoelectron microscopy (cryo-EM) structure of the ribosome indicated that these hypoxia-induced modifications stabilize the P-site and the PTC. These findings demonstrate that ribosomes are activated by hypoxia-induced modifications to enhance translational capability and thereby survival, under anaerobic conditions. PubMed: 41380683DOI: 10.1016/j.molcel.2025.11.018 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.59 Å) |
Structure validation
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