Fig. 2

Cryo-EM structure of ScRPA trimerisation core. a, b Cryo-EM reconstruction of ScRPA trimerisation core determined to 4.7 Å resolution by gold standard-FSC, post-processed and sharpened in Relion and colored by subunit; Rfa1 in blue, Rfa2 in pink, Rfa3 in pale green, and poly-dT in orange. c–e Orthogonal views of a fitted and refined homology model of ScRPA Tri-C. The subunits are colored as in a and a number of yeast-specific features in Rfa2 and Rfa3 that are expansions of the amino-acid polypeptide chain protrude and from loops that are visible in the cryo-EM map. The polypeptide chain linkers (missing in the structure) to the C-terminal winged-helix domain and N-terminal phosphorylation domain of Rfa2 are labeled, as well as the DbdB-DbdA and N-terminal domain of Rfa1. Scale bar represents ~70 Å. f Representative 2D-class averages showing an additional domain underneath the Tri-C that is positionally flexible. g Three individually refined maps from sub-classification of the data at sub-nanometer resolution, by gold standard-FSC (see Supplementary Fig 4), aligned on the Tri-C and fitted with 4.7 Å Tri-C map showing an additional small domain and its different locations in each map. The apparent domain motion is arrowed. Below, the highest resolution map (7.7 Å) with fitted atomic model from c showing that the additional density region is sufficient to fit an OB-fold. A homology model for DbdB is fitted and shown. Figures were generated in UCSF Chimera⁵⁶