(A) Model for the head-forming 3’ major domain (3’M; h28–h43) fitted into the cryo-EM density (left). The 3’M is divided into three blocks (block A, h29-h32; h38-h44, wheat; block B, h33-h34, light blue; block C, h35-h37, grey). The local resolution for block C and the major parts of the block A (h29-h32/h41-h43) is between 3.5 and 5.5 Å consistent with a stable and mature fold of these domains, whereas h39 and h40 and block B (h33–h34) are rather flexible, as indicated by a lower local resolution (right). Maps are low-pass filtered at 3.6 Å. (B) Model, density and local resolution of the central region of 18S rRNA connecting the 5’- (h1 and h2), central (h2 and h27), 3’M (h36) and the 3’m (h44) domains (left). h1 and h2 form the central pseudoknot (CPK; brown). While the 5’- and central domains as well as h36 form a rigid structure as indicated by high local resolution (middle left), h28 and the 3’m are more flexible and the entire linker region connecting h44 with h28 and h45 is not visible when low-pass filtered at 3.6 Å (left). Density for these flexible nucleotides (1633–1644 and 1754–1769; red) is only visible when low-pass filtering the map to below 15 Å (middle right). When compared to the mature state, h28 and h44 need to undergo a conformational transition. H28 is kinked by 13 degrees relative to its mature position and h44 is rotated outward towards the solvent side by 12 degrees (right). (C) view focusing on the rigid region around the CPK fitted into electron density (left). The connection between the 5’ and central domains to h36 of 3’M is already stably formed in the pre-40S particle as indicated by high local resolution below 3.5 Å, whereas h28 is more flexible (right).