Structure of a yeast spliceosome at 3.6-angstrom resolution

Abstract

Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing.

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

“…Structures of RRM-containing ribonucleoproteins and seminal spliceosome complexes (Yan et al 2015;Galej et al 2016;Rauhut et al 2016;Wan et al 2016a,b;Yan et al 2016) demonstrate that the RRM fold serves as a platform for multiprotein assemblies with RNA. One of the first RRM structures revealed distinct α-helical and β-sheet surfaces of the U2B ′′ RRM bound to the U2A ′ protein and the U2 small nuclear (sn) RNA (Price et al 1998).…”

Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

“…[38][39][40][41][42][43][44][45][46][47][48][49][50][51] However, recent efforts to determine high resolution cryo-EM density maps, utilizing advances in detector technology 52 coupled with powerful statistical image processing algorithms 53,54 have yielded structures for the U4/U6.U5 trisnRNP complex from S. cerevisiae [55][56][57] as well as the U5.U2/U6 intron lariat spliceosome (ILS) complex from S.pombe. [58][59][60] However, in the yeast U5.U2/U6 structure, the U2 snRNP region has an overall resolution of 11 A and lacks the density for the SF3b subcomplex. 58 The only structural data that is currently available for SF3b, although a low resolution cryo-EM density map, is that of human SF3b complex by Golas et.…”

Opening new doors for understanding eukaryotic RNA splicing

“…This embarrassing situation now gets to a turning point to catch up soon with other central dogma steps. The most recently solved spliceosome complex structure at near atomic resolution by professor Yigong Shi and his colleagues in Tsinghua University wipes off the fog and opens new doors for understanding RNA splicing in a new foreground [1,2].Almost all RNA transcripts in eukaryotic cells need additional processing steps before their maturation. The most critical processing step for messenger RNAs (mRNA) is the splicing, which removes the non-coding region (intron) and ligates the coding regions (exon) from a newly transcribed RNA to generate a mature RNA for translation.…”

“…This embarrassing situation now gets to a turning point to catch up soon with other central dogma steps. The most recently solved spliceosome complex structure at near atomic resolution by professor Yigong Shi and his colleagues in Tsinghua University wipes off the fog and opens new doors for understanding RNA splicing in a new foreground [1,2].…”

“…The new technology allowed the revelation of the spliceosome U4/U6.U5 tri-snRNP at 5.6 Å resolution for the first time [5]. Shi and his colleagues applied this new technology of cryo-electron microscopy to the spliceosome complex purified from cells using a modified protocol and solved the structure of the complex at 3.6 Å resolution [1]. In this structure, for the first time, we can see how proteins and snRNAs tangle together in a highly coordinated way and how the splicing active center is spatially organized among different snRNAs and the mRNA [2].…”