SNAP output for PDB entry 5mq0 [SNAP web server]

PDB-id

5mq0; SNAP-derived features in text and JSON formats; DNAproDB

Class

splicing

Method

cryo-EM (4.17 Å)

Summary

Structure of a spliceosome remodeled for exon ligation

Reference

Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K (2017): "Structure of a spliceosome remodelled for exon ligation." Nature, 542, 377-380. doi: 10.1038/nature21078.

Abstract

The spliceosome excises introns from pre-mRNAs in two sequential trans-esterifications - branching and exon ligation(1) - catalysed at a single catalytic metal site in U6 snRNA(2,3). The recent structures of the spliceosomal C complex(4,5) with the cleaved 5'-exon and lariat-3'-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5'-splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site(4). Here we present the 3.8 Å cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but prior to exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75 degrees compared to complex C and is stabilized into a new position by Prp17, Cef1, and the reoriented Prp8 RNaseH domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3'-exon docking, and restructures the pairing of the 5'-splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNaseH domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3'-exon, suggesting a possible basis for mRNA release after exon ligation(6,7). Together with the C complex structure(4), our new C* complex structure reveals the two major conformations of the spliceosome during the catalytic stages of splicing.