Figure 4.

Structural comparisons in the core region between the re-refined U4 core domain and U4prev (a) and between it and the minimal U1 snRNP (b, c). The backbone (C^α and P atoms) superposition is viewed from the tapered face of the ring. The re-refined U4 structure is shown in (a) and (b) in the molecular colour code of Fig. 3 ▸, while U4prev in (a) and U1 in (b) are coloured grey. In (a), the pocket in SmF is correctly occupied by A118 of U4 snRNA (magenta ladder) but is incorrectly occupied by G125 in U4prev (grey ladder). The register of the remaining Sm-site nucleotides relative to the Sm proteins was correct. The sequence-register error at the N-terminus of SmE in U4prev is now corrected. (b) shows the close agreement between U4 and U1 snRNP in the core region, except at the G→U substitution (U123 in U4 snRNA). (c) illustrates the U4–U1 backbone differences in the core region displayed as a colour ramp of pseudo-B factors along the U4 backbone trace. The colour ranges from blue for differences less than 0.2 Å, passing through white, to red for differences above 1.0 Å. The backbone differences are localized to the N- and C-termini of the proteins and at the U/G substitution in the Sm site. Loops L4 of SmB and SmD₂, which are divergent among NCS copies of the U4 structure, have been omitted from all of the comparisons.