Research Article: Re-refinement of the spliceosomal U4 snRNP core-domain structure

Date Published: January 01, 2016

Publisher: International Union of Crystallography

Author(s): Jade Li, Adelaine K. Leung, Yasushi Kondo, Chris Oubridge, Kiyoshi Nagai.


The structure of the spliceosomal U4 snRNP core domain has been re-refined following molecular replacement using the minimal U1 snRNP as a search model. RNA-omit maps show that the U4 Sm-site nucleotides AAUUUUU are bound to the seven Sm proteins SmF–SmE–SmG–SmD3–SmB–SmD1–SmD2 in the same manner as the U1 Sm-site nucleotides AAUUUGU except at the U-to-G substitution in SmD1.

Partial Text

The removal of noncoding sequences (introns) from precursor messenger RNA is an essential step in eukaryotic gene expression. It is catalysed by a large RNA–protein complex called the spliceosome (Wahl et al., 2009 ▸). The spliceosome is built up from five types of small nuclear ribonucleoprotein particles (U1, U2, U4, U5 and U6 snRNPs) and additional non-snRNP proteins in a defined order and hierarchy. Central to each snRNP is its eponymous snRNA molecule. In the U1, U2, U4 and U5 snRNPs, a common set of seven Sm proteins (SmB/SmB′, SmD1, SmD2, SmD3, SmE, SmF and SmG) bind as a ring around a single-stranded, semiconserved U-rich sequence PuAU4–6(G/U)Pu called the Sm site within the snRNA, forming the snRNP core domain (Yu et al., 1999 ▸; Pettersson et al., 1984 ▸; Bringmann & Lührmann, 1986 ▸). Core-domain formation is a prerequisite for import into the nucleus, where the snRNPs mature after recruiting particle-specific proteins. We initiated the crystallographic study of the U4 snRNP core domain in order to understand the recognition of the semiconserved Sm-site sequences by a common set of Sm proteins and the selection of snRNP-specific proteins by the assembled core domain.




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