8XTP image
Entry Detail
PDB ID:
8XTP
EMDB ID:
Keywords:
Title:
Comamonas testosteroni KF-1 circularly permuted group II intron Post-2S state
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2024-01-11
Release Date:
2025-02-12
Method Details:
Experimental Method:
Resolution:
2.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:RNA (133-MER)
Chain IDs:B (auth: A)
Chain Length:133
Number of Molecules:1
Biological Source:Comamonas testosteroni KF-1
Polymer Type:polyribonucleotide
Description:RNA (595-MER)
Chain IDs:A (auth: B)
Chain Length:595
Number of Molecules:1
Biological Source:Comamonas testosteroni KF-1
Primary Citation
Structural basis of circularly permuted group II intron self-splicing.
Nat.Struct.Mol.Biol. ? ? ? (2025)
PMID: 39890981 DOI: 10.1038/s41594-025-01484-x

Abstact

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, M35, 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.

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