8CVJ
Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMSEAC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution
This is a non-PDB format compatible entry.
Summary for 8CVJ
| Entry DOI | 10.2210/pdb8cvj/pdb |
| Descriptor | 23S Ribosomal RNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (62 entities in total) |
| Functional Keywords | 70s ribosome, non-hydrolyzable, aminoacyl-trna, peptidyl-trna, formylation, pre-attack state, transpeptidation, peptidyl transferase center, nascent peptide exit tunnel, ribosome, ribosome-rna complex, ribosome/rna |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 114 |
| Total formula weight | 4570935.99 |
| Authors | Syroegin, E.A.,Aleksandrova, E.V.,Polikanov, Y.S. (deposition date: 2022-05-18, release date: 2022-10-19, Last modification date: 2023-11-15) |
| Primary citation | Syroegin, E.A.,Aleksandrova, E.V.,Polikanov, Y.S. Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes. Nat.Chem., 15:143-153, 2023 Cited by PubMed Abstract: During protein synthesis, the growing polypeptide threads through the ribosomal exit tunnel and modulates ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics, appearing in the tunnel. While arrested ribosome-nascent chain complexes (RNCCs) have been extensively studied structurally, the lack of a simple procedure for the large-scale preparation of peptidyl-tRNAs, intermediates in polypeptide synthesis that carry the growing chain, means that little attention has been given to RNCCs representing functionally active states of the ribosome. Here we report the facile synthesis of stably linked peptidyl-tRNAs through a chemoenzymatic approach based on native chemical ligation and use them to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase centre. These structures reveal that C-terminal parts of the growing peptides adopt the same uniform β-strand conformation stabilized by an intricate network of hydrogen bonds with the universally conserved 23S rRNA nucleotides, and explain how the ribosome synthesizes growing peptides containing various sequences with comparable efficiencies. PubMed: 36316410DOI: 10.1038/s41557-022-01073-1 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.4 Å) |
Structure validation
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