8X9K

Cte_Branching,Ca,inactive

8X9K の概要

• エントリーDOI: 10.2210/pdb8x9k/pdb
• EMDBエントリー: 38173
• 分子名称: RNA (808-MER), CALCIUM ION, POTASSIUM ION, ... (4 entities in total)
• 機能のキーワード: cp group ii intron, cte, back-splicing, circular rna, cryo-em, splicing, rna
• 由来する生物種: Comamonas testosteroni KF-1
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 263825.48

構造登録者

Ling, X.B.,Ma, J.B. (登録日: 2023-11-30, 公開日: 2025-03-12, 最終更新日: 2025-06-25)

主引用文献

Ling, X.,Yao, Y.,Ma, J.
Structures of a natural circularly permuted group II intron reveal mechanisms of branching and backsplicing.
Nat.Struct.Mol.Biol., 32:1101-1110, 2025

PubMed Abstract: Circularly permuted (CP) group II introns, identified in various bacteria phyla, swap domains D5 and D6 near the 5' end and have reversed splice sites (SSs), leading to backsplicing and circular RNA formation. In this study, we present multiple high-resolution cryo-electron microscopy structures of a natural CP group II intron from Comamonas testosteroni KF-1 (Cte 1), elucidating the molecular mechanisms of branching and backsplicing. During branching, the 5' SS is positioned by an auxiliary sequence (AUX)-enhanced interaction between the exon-binding site and intron-binding site (IBS) and stacks on the branch-site adenosine within D6, allowing the attacking 2'-OH group to coordinate with a metal ion in the active center. In backsplicing, the 3' SS is aligned with the branching step, leaving IBS in the active center, stabilized by base pairing with the AUX, which enables the free 3'-end hydroxyl group to directly attack the scissile phosphate of 3' SS. Furthermore, a groove in Cte 1 may stabilize the circular RNA. These findings highlight a conserved catalytic mechanism for canonical group II introns, albeit facilitated by the versatile AUX, opening avenues for designing potent ribozymes producing circular RNAs.

PubMed: 40016344
DOI: 10.1038/s41594-025-01489-6

実験手法

ELECTRON MICROSCOPY (2.63 Å)