Extended Data Figure 5: Protein structures in the 39S subunit.

a, mL37 (green) and mL65 (MRPS30; blue) bound to the 39S subunit (16S rRNA backbone in orange; other mitoribosomal proteins in grey). b, mL37 and mL65 (MRPS30) form a pseudo-dimeric assembly on the 39S subunit. c, Superposition of mL37 and mL65 (MRPS30), revealing their common core fold with additional extensions specific to each protein. d, Segment of the mL65 (MRPS30) structure shown in the cryo-EM map (only density corresponding to the selected structural element is shown). Side chain densities can be clearly identified and allowed the identification of the register of the mL65 (MRPS30) sequence in the map. e, Two CX-MS crosslinks between mL65 (MRPS30) and mL37 confirm the placement of mL65 (MRPS30) on the 39S subunit (red, DSS crosslink between lysines; gold, PDH crosslink between carboxyl groups). f, Crosslinks with other mitoribosomal proteins. DSS crosslinks of mL37 with uL2m (purple) and uL29m (gold) and of mL65 (MRPS30) with mL41 (cyan) were observed. All crosslink Cα–Cα distances are 22 Å or shorter. g, Binding site of mL66 (MRPS18A) at the L7/L12 stalk base. mL66 (MRPS18A; gold) and neighbouring mL53 (purple) form a joint β-sheet. h, Side-chain density allows the unambiguous assignment of the location and trace of mL66 (MRPS18A). i, Semi-quantitative MS analysis of protein abundance in the 55S mitoribosome. mL66 (MRPS18A) and mL65 (MRPS30) are present in roughly stoichiometric amounts with other 39S subunit proteins, indicating that only one copy is present per 55S mitoribosome. Only bL12m was detected with clearly more than one copy per 55S mitoribosome, as expected from the multimeric architecture of the L7/L12 stalk⁵⁸. j, Top view of the CP. In addition to the mitochondrial-specific CP tRNA, several mitochondrial-specific proteins have been recruited to the strongly remodelled CP of the 39S subunit. k, Side view of the CP. Owing to the missing 5S rRNA, the CP is connected to the subunit main body exclusively by protein contacts. l, Structure of the L7/L12 stalk base. Mitochondrial-specific ribosomal proteins mL53, mL54 and mL66 (MRPS18A) have been recruited to the L7/L12 stalk base and may stabilize its connection to the 39S subunit main body.