Supplementary Figure 4: Cryo-EM analysis of the Yvh1 pre-60S particle.

(a) Model of the Yvh1 phosphatase domain fit into the cryo-EM density of the Yvh1 pre-60S particle contacting ribosomal protein Rpl12. The phosphatase domain of Yvh1 was modeled on PDB ID: 2OUD (Tao, X. et al., Protein Sci. 16, 880-886, 2007); the model of Rpl12 was taken from PDB ID: 4V7F (Leidig, C. et al., Nat Commun 5 , 3491, 2014). (b) View on the position of Rpl10, based on the structure of a mature 60S subunit taken from PDB ID: 4V88 (Ben-Shem, A. et al., Science 334 , 1524-1529, 2011) into the density of the Yvh1 particle, revealing that ribosomal Rpl10 is absent in the Yvh1 particle. (c) Positions of the helices H68, H69 and H71 in the early Arx1 particle (blue) and a mature 60S subunit (dark red). Models of the complete ribosomal RNA (PDB ID: 4V7F and PDB ID: 4V88) were fit into the density of the Yvh1 particle. There are no distinct densities visible for H68 and H69, whereas H71 is located in its mature position. (d and e) View on the 5.8S rRNA region in the Yvh1 particle (d) with the Mex67 crosslink hits to helices H7, H9-H10 (red) as compared to the early Arx1 particle (e) (EMD-2528; Leidig, C. et al., Nat Commun 5 , 3491, 2014), where CRAC hits of Mtr4 (pink) and Nop53 (cyan) are indicated.