9DTR

Structure of the yeast post-catalytic P complex spliceosome at 2.3 Angstrom resolution

Summary for 9DTR

• Entry DOI: 10.2210/pdb9dtr/pdb
• EMDB information: 47157
• Descriptor: U2 snRNA, UBC4 lariat-intron, Pre-mRNA-splicing factor PRP46, ... (43 entities in total)
• Functional Keywords: spliceosome, snrna, yeast, ribonucleoprotein complex, splicing
• Biological source: Saccharomyces cerevisiae (brewer's yeast); More
• Total number of polymer chains: 47
• Total formula weight: 2280691.71

Authors

Wilkinson, M.E.,Hoskins, A.A. (deposition date: 2024-10-01, release date: 2024-12-25, Last modification date: 2026-06-17)

Primary citation

Senn, K.A.,Lipinski, K.A.,Zeps, N.J.,Griffin, A.F.,Wilkinson, M.E.,Hoskins, A.A.
Control of 3' splice site selection by the yeast splicing factor Fyv6.
Elife, 13:-, 2024

PubMed Abstract: Pre-mRNA splicing is catalyzed in two steps: 5' splice site (SS) cleavage and exon ligation. A number of proteins transiently associate with spliceosomes to specifically impact these steps (first and second step factors). We recently identified Fyv6 (FAM192A in humans) as a second step factor in ; however, we did not determine how widespread Fyv6's impact is on the transcriptome. To answer this question, we have used RNA sequencing (RNA-seq) to analyze changes in splicing. These results show that loss of Fyv6 results in activation of non-consensus, branch point (BP) proximal 3' SS transcriptome-wide. To identify the molecular basis of these observations, we determined a high-resolution cryo-electron microscopy (cryo-EM) structure of a yeast product complex spliceosome containing Fyv6 at 2.3 Å. The structure reveals that Fyv6 is the only second step factor that contacts the Prp22 ATPase and that Fyv6 binding is mutually exclusive with that of the first step factor Yju2. We then use this structure to dissect Fyv6 functional domains and interpret results of a genetic screen for suppressor mutations. The combined transcriptomic, structural, and genetic studies allow us to propose a model in which Yju2/Fyv6 exchange facilitates exon ligation and Fyv6 promotes usage of consensus, BP distal 3' SS.

PubMed: 39688371
DOI: 10.7554/eLife.100449

Experimental method

ELECTRON MICROSCOPY (2.31 Å)