Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome

Abstract

The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ATP generation for the eukaryotic cell. The mammalian 55S mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins and an additional 35 mito-specific MRPs. Here we present the cryo-EM structure analysis of the small (28S) subunit (SSU) of the 55S mitoribosome. We find that the mito-specific extensions in homologous MRPs generally are involved in inter-MRP contacts and in contacts with mito-specific MRPs, suggesting a stepwise evolution of the current architecture of the mitoribosome. Although most of the mito-specific MRPs and extensions of homologous MRPs are situated on the peripheral regions, they also contribute significantly to the formation of linings of the mRNA and tRNA paths, suggesting a tailor-made structural organization of the mito-SSU for the recruitment of mito-specific mRNAs, most of which do not possess a 5' leader sequence. In addition, docking of previously published coordinates of the large (39S) subunit (LSU) into the cryo-EM map of the 55S mitoribosome reveals that mito-specific MRPs of both the SSU and LSU are involved directly in the formation of six of the 15 intersubunit bridges.

Keywords: cryo-electron microscopy; mammalian MRPs; mammalian mitochondrial ribosomal SSU; mito-12S rRNA.

Fig. 1.

Cryo-EM structure of the mammalian mitochondrial 28S ribosomal SSU. (A and B) Segmented cryo-EM densities for 12S rRNA (gray), homologous MRPs (green), mito-specific extensions and insertions in homologous MRPs (red), and mito-specific MRPs (yellow). Landmarks: h, head; b, body; pt, platform; bl, beak lobe; lbf, lower body finger. (C and D) The 28S structure with modeled 12S rRNA (gray) and 15 homologous MRPs. Densities tentatively assigned to mito-specific MRPs (S23, S25–S31, S33–S35, and S37), along with their docked homology models, are shown as meshwork (also see Table S2 and Figs. S3–S5). Densities shown as solid yellow did not match homology models but also have been tentatively assigned, and densities marked with asterisks (*) would correspond to undocked portions of MRP S27 and S30 models. The mito-SSU is shown from the interface side in A and C and from the solvent side in B and D.

Fig. 2.

Molecular interactions in the mito-SSU body. Environments of (A) NTE (red) of MRP S5 and (B) NTEs and CTEs of MRPs S15 (green) and S17 (sea green). Here and in subsequent figures, NTEs and CTEs of MRPs are indicated by the suffix “n” or “c”, respectively, in matching colors. “h” followed by a number indicates the 12 rRNA helix. As in Fig. 1 C and D, docked models of mito-specific MRPs are shown along with their cryo-EM densities (meshwork), and undocked densities are shown as solid masses in this and subsequent figures. Thumbnails to the left in this and subsequent figures show the overall orientations of the mito-SSU.

Fig. 3.

Depiction of possible effect of a nonsense mutation within the mito-specific CTE in MRP S16. (A) Close-up view of the S16 CTE region (red). (B) As in A, but the expected truncated part of the S16 CTE because the mutation of Arg111 (R111) to a stop codon has been removed computationally.

Fig. 4.

Molecular interactions in the mito-SSU head involving MRPs S10, S14, and S24.

Fig. 5.

Molecular architectures of the mRNA entrance and exit regions and interactions in the mito-SSU platform. (A and B) The mRNA entrance is shown from two different orientations (from the solvent side in A, and from the shoulder side in B) to reveal better the features of the mRNA gate, which is composed primarily of the NTE of MRP S5 (S5n) and MRP S39. (C) The mRNA exit region. The 3′ and 5′ ends of the modeled mRNA (28) are shown as thick purple ribbons.

Fig. 6.

Location and composition of the intersubunit bridges between the two mitoribosomal subunits. (A) Structure of the 55S mitoribosome, with docked models of mitochondrial SSU (Left) and LSU (Right). The cryo-EM density is shown as semitransparent gray meshwork. Head (h) and body (b) of the mito-SSU and the central protuberance (CP) and L11 Stalk base region (Sb) of the mito-LSU are labeled. (B and C) SSU (B) and LSU (C) are shown from their interface sides to reveal intersubunit bridges. Bridges involving conserved RNA–RNA segments (purple), conserved protein–protein (blue), RNA–protein (red), and between two mito-specific MRPs (black) are highlighted. The two asterisks indicate the locations of bridges B1a and B1b, which most likely involve unmodeled segments of the same mito-specific MRP of the SSU that forms bridges B1c and B1d. rRNAs of the SSU and LSU are shown in orange and pink, respectively, in A; in B and C they are shown in gray to enhance bridges. Homologous MRPs of both subunits are shown in different shades of green. Mito-specific MRPs of the SSU and LSU are shown in yellow and blue, respectively.