Crystal Structure of a Ten-Subunit Human Spliceosomal U1 snRNP at 5.5 Å Resolution

Most eukaryotic protein-coding genes contain non-coding regions (introns) that separate those coding for protein (exons). The introns must be excised and exons spliced together from the precursor-mRNA transcript of such genes. This process (RNA splicing) is catalyzed by the spliceosome, integral to which are five RNA-protein complexes (U1, U2, U4, U5 and U6 snRNPs). A first step in RNA splicing, functioning to initiate spliceosome assembly, involves recognition of the junction between the 5′-exon and intron (5′-splice site) by U1 snRNP. Human U1 snRNP (∼250 kDa) is composed of one RNA (U1 snRNA) and ten polypeptides (seven Sm proteins, U1-A, U1-70K, and U1-C). An experimental electron density map at 5.5 A resolution enabled us to build U1 snRNA and, in conjunction with site-specific labeling of individual proteins, to place the seven Sm proteins, U1-C and U1-70K into the map. The structure reveals a hierarchical network of interactions between subunits. The seven Sm proteins interact to form a heptameric ring with a single-stranded segment of U1 snRNA leafing through its center. Sm proteins form multiple and varied interactions, with other regions of U1 snRNA as well as other protein subunits, to stabilize the structure of the particle overall. A striking feature is the amino terminus of one subunit (U1-70K), which extends over a distance of ∼180 A, wrapping around the Sm protein heptameric ring, to contact the protein U1-C. The U1-C protein is crucial for 5′-splice-site recognition. In the crystal, the zinc-finger of U1-C interacts with an RNA duplex formed between the single-stranded 5′-end of U1 snRNA and its counterpart from an adjacent complex. This unexpected interaction provides important insight into the critical role of U1-C in recognizing the precursor-mRNA transcript 5′-splice site.