Extended Data Figure 6: 3D RNA network of the human C* complex.

a, b, Fit of the catalytic core RNA into the 5.9 Å EM density map of C* (a) or into the EM density map low-pass filtered to 4.5 Å (b). The topography of the RNA density is consistent with formation of the catalytic triplex, as found in the C complex and ILS. That is, the Watson–Crick faces of U6 nucleotides G46 and A47 are oriented towards the Hoogsteen faces of G54 and A53, respectively, and can potentially form two base triples. The bulged U74 of the U6 ISL would be in a position to stack on G46 and may form the third triple with U6 C55 (Fig. 2). Black circle, catalytic centre. c, Overall similarity of the catalytic RNA network in the yeast C versus human C* complex. Superimposition of the core RNA elements from human C* with those from the S. cerevisiae C complex. Dark-coloured RNAs are from C*, whereas the lighter-coloured RNAs are from the C complex (PDB 5LJ3) and (PDB 5GMK). In the C* complex, the U6 ACAGA box/intron helix is tilted slightly (compared to the C complex), such that the U6 snRNA moves 5–6 Å towards the core of the complex, which is probably due to the significantly different positions of the branched intron structures in the different spliceosomal complexes. d, The conformation of U6 nucleotide A48 (U54 in yeast U6) is significantly different in the yeast C and human C* complex. Whether U6 A48 adopts this distinct conformation in other human spliceosomal complexes or whether it represents an intermediate state following PRP16 remodelling that subsequently adopts a conformation similar to U6 U54 in the yeast C complex before step two catalysis is unclear. e, U6 A48 is bound in a protein pocket comprised of amino acids from Skip and CDC5. Fit of U6 and U2 snRNA nucleotides, and amino acids of CDC5 and Skip into the C* EM density map. f, Interactions of the U5 loop 1 and PRP8 with the 5′ exon, and location of the 3′ end of the 5′ exon close to the catalytic centre (black circle).