9V7N

Cryo-EM structures of the Azoarcus pre-tRNA(ILE) conformation a undergoing the first-step self-splicing

Summary for 9V7N

• Entry DOI: 10.2210/pdb9v7n/pdb
• EMDB information: 64818
• Descriptor: RNA (284-MER), GUANOSINE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: azoarcus pre-trna(ile), self-splicing, pre-1s, rna structure, rna
• Biological source: Azoarcus olearius
• Total number of polymer chains: 3
• Total formula weight: 276013.52

Authors

Hong, Y.,Liu, J.,Zhang, X.,Liu, J.,Li, S.,Zhang, K. (deposition date: 2025-05-28, release date: 2026-03-25, Last modification date: 2026-04-08)

Primary citation

Hong, Y.,Liu, J.,Zhang, X.,Liu, J.,Li, S.,Zhang, K.
Pre-splicing conformation and stepwise circularization of a group I intron in Azoarcus pre-tRNA.
Nat Commun, 2026

PubMed Abstract: Group I introns are catalytic RNAs capable of self-splicing, yet structural insights into full-length precursor RNAs and post-splicing circularization have been limited. Here, we present cryo-EM structures of the Azoarcus pre-tRNA system across key catalytic stages, including the full-length precursor in Pre-1S conformations, the linear intron, and the circular introns, at 2.8-3.3 Å resolution. These structures reveal a preformed P1 helix, register shifts during splicing, and a conformational flip of G37 that stabilizes the circularization site. Biochemical analyses confirm a two-step circularization mechanism, generating a secondary circular product via an alternative ligation site. Together, our results provide an atomic-level view of a group I intron system through splicing and circularization. This work uncovers structural principles governing RNA conformational dynamics, catalysis, and circular RNA formation, with broad implications for ribozyme engineering.

PubMed: 41862486
DOI: 10.1038/s41467-026-70747-y

Experimental method

ELECTRON MICROSCOPY (3.11 Å)