8XTP

Comamonas testosteroni KF-1 circularly permuted group II intron Post-2S state

Summary for 8XTP

• Entry DOI: 10.2210/pdb8xtp/pdb
• EMDB information: 38646
• Descriptor: RNA (595-MER), RNA (133-MER), POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: cryoem, ribozyme, rna
• Biological source: Comamonas testosteroni KF-1; More
• Total number of polymer chains: 2
• Total formula weight: 237720.97

Authors

Wang, L.,Xie, J.H.,Zhang, C.,Zou, J.,Huang, Z.R.,Shang, S.T.,Chen, X.Y.,Yang, Y.,Liu, J.,Dong, H.H.,Huang, D.M.,Su, Z.M. (deposition date: 2024-01-11, release date: 2025-02-12, Last modification date: 2025-07-23)

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., 32:1091-1100, 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 (2.9 Å)