8HSP

E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A37 in classical state

これはPDB形式変換不可エントリーです。

8HSP の概要

• エントリーDOI: 10.2210/pdb8hsp/pdb
• EMDBエントリー: 35001
• 分子名称: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (57 entities in total)
• 機能のキーワード: trna modification, decoding, ribosome
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 55
• 化学式量合計: 2213137.82

構造登録者

Akiyama, N.,Ishiguro, K.,Yokoyama, T.,Shirouzu, M.,Suzuki, T. (登録日: 2022-12-20, 公開日: 2024-04-03, 最終更新日: 2025-12-24)

主引用文献

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

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: 38538915
DOI: 10.1038/s41594-024-01238-1

実験手法

ELECTRON MICROSCOPY (2.32 Å)