9NO7
Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-N5-methylated Release Factor 1, and P-site 2'-deoxy-A76-fMEAAAKC-peptidyl-tRNAcys at 2.13A resolution
This is a non-PDB format compatible entry.
Summary for 9NO7
| Entry DOI | 10.2210/pdb9no7/pdb |
| EMDB information | 49594 |
| Descriptor | 23S Ribosomal RNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (61 entities in total) |
| Functional Keywords | translation termination; peptide release; release factor; hydrolysis; peptidyl-trna; 70s ribosome; cryo-em; pre-termination state; peptidyl transferase center, ribosome |
| Biological source | Thermus thermophilus HB8 More |
| Total number of polymer chains | 56 |
| Total formula weight | 2284871.18 |
| Authors | Aleksandrova, E.V.,Syroegin, E.A.,Basu, R.S.,Vassilevski, A.A.,Gagnon, M.G.,Polikanov, Y.S. (deposition date: 2025-03-08, release date: 2025-06-18, Last modification date: 2025-07-02) |
| Primary citation | Aleksandrova, E.V.,Syroegin, E.A.,Basu, R.S.,Vassilevski, A.A.,Gagnon, M.G.,Polikanov, Y.S. Mechanism of release factor-mediated peptidyl-tRNA hydrolysis on the ribosome. Science, 388:eads9030-eads9030, 2025 Cited by PubMed Abstract: Translation termination is essential in all living organisms because it ensures that proteins have lengths strictly defined by their genes. This universal process is mediated by peptide release factors (RFs) that recognize stop codons and catalyze the hydrolysis of peptidyl transfer RNA (peptidyl-tRNA) on the ribosome, presumably by activating a water molecule. We report structures of the bacterial ribosome in complex with peptidyl-tRNA and RFs in the prepeptide release state. No hydrolytic water molecule was seen in the peptidyl transferase center. Instead, RFs induced rearrangements of the peptidyl-tRNA adenine 76 (A76) ribose pucker that orient the 2'-OH for the nucleophilic attack onto the neighboring carbonyl group. These findings suggest a catalytic mechanism of RF-mediated peptide release and provide a structural basis for the universal conservation of the catalytic domain in peptide RFs. PubMed: 40536958DOI: 10.1126/science.ads9030 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.13 Å) |
Structure validation
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