8HTZ
E. coli 70S ribosome complexed with H. marismortui tRNA_Ile2 bearing agm2C34 in classical state
This is a non-PDB format compatible entry.
Summary for 8HTZ
| Entry DOI | 10.2210/pdb8htz/pdb |
| EMDB information | 35020 |
| Descriptor | 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (57 entities in total) |
| Functional Keywords | trna modification, decoding, ribosome |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 55 |
| Total formula weight | 2213753.72 |
| Authors | Akiyama, N.,Ishiguro, K.,Yokoyama, T.,Shirouzu, M.,Suzuki, T. (deposition date: 2022-12-22, release date: 2024-04-03, Last modification date: 2025-02-12) |
| Primary citation | Akiyama, N.,Ishiguro, K.,Yokoyama, T.,Miyauchi, K.,Nagao, A.,Shirouzu, M.,Suzuki, T. Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine. Nat.Struct.Mol.Biol., 31:817-825, 2024 Cited by PubMed Abstract: The anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and agmatidine (agmC), respectively, in the anticodon of tRNA to decipher AUA codon. L and agmC contain long side chains with polar termini, but their functions remain elusive. Here we report the cryogenic electron microscopy structures of tRNAs recognizing the AUA codon on the ribosome. Both modifications interact with the third adenine of the codon via a unique C-A geometry. The side chains extend toward 3' direction of the mRNA, and the polar termini form hydrogen bonds with 2'-OH of the residue 3'-adjacent to the AUA codon. Biochemical analyses demonstrated that AUA decoding is facilitated by the additional interaction between the polar termini of the modified cytidines and 2'-OH of the fourth mRNA residue. We also visualized cyclic N-threonylcarbamoyladenosine (ctA), another tRNA modification, and revealed a molecular basis how ctA contributes to efficient decoding. PubMed: 38538915DOI: 10.1038/s41594-024-01238-1 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.4 Å) |
Structure validation
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