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Structure paper

TitleStructural basis of circularly permuted group II intron self-splicing.
Journal, issue, pagesNat Struct Mol Biol, Vol. 32, Issue 6, Page 1091-1100, Year 2025
Publish dateJan 31, 2025
AuthorsLiu Wang / Jiahao Xie / Chong Zhang / Jian Zou / Zirui Huang / Sitong Shang / Xingyu Chen / Yang Yang / Jianquan Liu / Haohao Dong / Dingming Huang / Zhaoming Su /
PubMed AbstractCircularly 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. ...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.
External linksNat Struct Mol Biol / PubMed:39890981
MethodsEM (single particle)
Resolution2.54 - 2.96 Å
Structure data

38646

8xtp

EMDB-38646, PDB-8xtp:
Comamonas testosteroni KF-1 circularly permuted group II intron Post-2S state
Method: EM (single particle) / Resolution: 2.9 Å

38647

8xtq

EMDB-38647, PDB-8xtq:
Comamonas testosteroni KF-1 circularly permuted group II intron 1S state
Method: EM (single particle) / Resolution: 2.96 Å

38648

8xtr

EMDB-38648, PDB-8xtr:
Comamonas testosteroni KF-1 circularly permuted group II intron 2S state
Method: EM (single particle) / Resolution: 2.67 Å

38649

8xts

EMDB-38649, PDB-8xts:
Comamonas testosteroni KF-1 circularly permuted group II intron Pre-1S state
Method: EM (single particle) / Resolution: 2.54 Å

60833

9is7

EMDB-60833, PDB-9is7:
Paracandidimonas lactea CP group II intron 2S state
Method: EM (single particle) / Resolution: 2.87 Å

Chemicals

ChemComp-K:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-SPD:
SPERMIDINE

Source
  • comamonas testosteroni kf-1 (bacteria)
  • paracandidimonas lactea (bacteria)
KeywordsRNA / CryoEM / Ribozyme

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