8XTR
Comamonas testosteroni KF-1 circularly permuted group II intron 2S state
Summary for 8XTR
| Entry DOI | 10.2210/pdb8xtr/pdb |
| EMDB information | 38648 |
| Descriptor | RNA (219-MER), RNA (595-MER), POTASSIUM ION, ... (4 entities in total) |
| Functional Keywords | cryoem, ribozyme, rna |
| Biological source | Comamonas testosteroni KF-1 More |
| Total number of polymer chains | 2 |
| Total formula weight | 265159.95 |
| Authors | |
| 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 Cited by 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: 39890981DOI: 10.1038/s41594-025-01484-x PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.67 Å) |
Structure validation
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