9IS7

Paracandidimonas lactea CP group II intron 2S state

Summary for 9IS7

• Entry DOI: 10.2210/pdb9is7/pdb
• EMDB information: 60833
• Descriptor: RNA (153-MER), RNA (582-MER), MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: cryoem, ribozyme, rna
• Biological source: Paracandidimonas lactea; More
• Total number of polymer chains: 2
• Total formula weight: 239697.27

Authors

Wang, L.,Xie, J.H.,Zhang, C.,Zou, J.,Huang, Z.,Shang, S.,Chen, X.,Yang, Y.,Liu, J.,Dong, H.,Huang, D.,Su, Z. (deposition date: 2024-07-17, release date: 2025-02-12)

Primary citation

Wang, L.,Xie, J.,Zhang, C.,Zou, J.,Huang, Z.,Shang, S.,Chen, X.,Yang, Y.,Liu, J.,Dong, H.,Huang, D.,Su, Z.
Structural basis of circularly permuted group II intron self-splicing.
Nat.Struct.Mol.Biol., 2025

PubMed Abstract: Circularly permuted group II introns (CP introns) consist of rearranged structural domains separated by two tethered exons, generating branched introns and circular exons via back-splicing. Structural and mechanistic understanding of circular RNA (circRNA) generation by CP introns remains elusive. We resolve cryo-electron microscopy structures of a natural CP intron in different states during back-splicing at a resolution of 2.5-2.9 Å. Domain 6 (D6) undergoes a conformational change of 65° after branching, to facilitate 3'-exon recognition and circularization. Previously unseen tertiary interactions compact the catalytic triad and D6 for splicing without protein, whereas a metal ion, M, is observed to stabilize the 5'-exon during splicing. While these unique features were not observed in canonical group II introns and spliceosomes, they are common in CP introns, as demonstrated by the cryo-EM structure of another CP intron discovered by comparative genomics analysis. Our results elucidate the mechanism of CP intron back-splicing dynamics, with potential applications in circRNA research and therapeutics.

PubMed: 39890981
DOI: 10.1038/s41594-025-01484-x

Experimental method

ELECTRON MICROSCOPY (2.87 Å)