Sm protein–Sm site RNA interactions within the inner ring of the spliceosomal snRNP core structure

Seven Sm proteins, E, F, G, D1, D2, D3 and B/B′, assemble in a stepwise manner onto the single‐stranded Sm site element (PuAU 4–6 GPu) of the U1, U2, U4 and U5 spliceosomal snRNAs, resulting in a doughnut‐shaped core RNP structure. Here we show by UV cross‐linking experiments using an Sm site RNA oligonucleotide (AAGA) that several Sm proteins contact the Sm site RNA, with the most efficient cross‐links observed for the G and B/B′ proteins. Site‐specific photo‐cross‐linking revealed that the G and B/B′ proteins contact distinct uridines (in the first and third positions, respectively) in a highly position‐specific manner. Amino acids involved in contacting the RNA are located at equivalent regions in both proteins, namely in loop L3 of the Sm1 motif, which has been predicted to jut into the hole of the Sm ring. Our results thus provide the first evidence that, within the core snRNP, multiple Sm protein–Sm site RNA contacts occur on the inner surface of the heptameric Sm protein ring.