8CEC
Rnase R bound to a 30S degradation intermediate (State I - head-turning)
Summary for 8CEC
| Entry DOI | 10.2210/pdb8cec/pdb |
| Related | 8CDU 8CDV |
| EMDB information | 16595 16596 16605 |
| Descriptor | 16S rRNA, 30S ribosomal protein S16, 30S ribosomal protein S17, ... (22 entities in total) |
| Functional Keywords | ssu, 30s, rnase r, ribosomal degradation, turnover, ribosome |
| Biological source | Bacillus subtilis subsp. subtilis str. 168 More |
| Total number of polymer chains | 22 |
| Total formula weight | 867869.82 |
| Authors | Paternoga, H.,Dimitrova-Paternoga, L.,Wilson, D.N. (deposition date: 2023-02-01, release date: 2023-12-20, Last modification date: 2024-10-23) |
| Primary citation | Dimitrova-Paternoga, L.,Kasvandik, S.,Beckert, B.,Granneman, S.,Tenson, T.,Wilson, D.N.,Paternoga, H. Structural basis of ribosomal 30S subunit degradation by RNase R. Nature, 626:1133-1140, 2024 Cited by PubMed Abstract: Protein synthesis is a major energy-consuming process of the cell that requires the controlled production and turnover of ribosomes. Although the past few years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3' to 5' exonuclease ribonuclease R (RNase R). The structures reveal that RNase R binds at first to the 30S platform to facilitate the degradation of the functionally important anti-Shine-Dalgarno sequence and the decoding-site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S subunit, and this is overcome by a major structural rearrangement of the 30S head, involving the loss of ribosomal proteins. RNase R parallels this movement and relocates to the decoding site by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also indicate that the enzyme alone is sufficient for complete degradation of 30S subunits. Collectively, our results provide a mechanistic basis for the degradation of 30S mediated by RNase R, and reveal that RNase R targets orphaned 30S subunits using a dynamic mechanism involving an anchored switching of binding sites. PubMed: 38326618DOI: 10.1038/s41586-024-07027-6 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.57 Å) |
Structure validation
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