Summary for 8QCQ
| Entry DOI | 10.2210/pdb8qcq/pdb |
| EMDB information | 18332 |
| Descriptor | 50S ribosomal protein L32, 50S ribosomal protein L3, 50S ribosomal protein L4, ... (54 entities in total) |
| Functional Keywords | stalling, nascent chain, elongation arrest, regulation, ribosome |
| Biological source | Amycolatopsis japonica More |
| Total number of polymer chains | 50 |
| Total formula weight | 2105870.36 |
| Authors | Morici, M.,Wilson, D.N. (deposition date: 2023-08-28, release date: 2024-03-20, Last modification date: 2025-03-12) |
| Primary citation | Morici, M.,Gabrielli, S.,Fujiwara, K.,Paternoga, H.,Beckert, B.,Bock, L.V.,Chiba, S.,Wilson, D.N. RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Nat Commun, 15:2432-2432, 2024 Cited by PubMed Abstract: Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies. PubMed: 38503735DOI: 10.1038/s41467-024-46761-3 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.3 Å) |
Structure validation
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