Ribosome. The structure of the human mitochondrial ribosome

Abstract

The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-particle electron cryogenic microscopy. It reveals 80 extensively interconnected proteins, 36 of which are specific to mitochondria, and three ribosomal RNA molecules. The head domain of the small subunit, particularly the messenger (mRNA) channel, is highly remodeled. Many intersubunit bridges are specific to the mitoribosome, which adopts conformations involving ratcheting or rolling of the small subunit that are distinct from those seen in bacteria or eukaryotes. An intrinsic guanosine triphosphatase mediates a contact between the head and central protuberance. The structure provides a reference for analysis of mutations that cause severe pathologies and for future drug design.

Fig. 1. Map quality

A. Maps generated using masked refinement colored by local resolution. The outline of the mask applied to the head is shown as a dashed line. Colored circles pinpoint the location on the mt-SSU of the density examples shown in panels B-D. B. Density for mS27 at the bottom of the mt-SSU. C. Well-resolved density for mS38 in the core of the mt-SSU. D. Density for mS29 including the bound GDP at the head.

Fig. 2. Overview of the human mitoribosome

A. Proteins conserved with bacteria (blue), extensions of homologous proteins (yellow) and mitochondria-specific proteins (red). rRNA is shown in gray. B. Location of proteins in the human mt-SSU.

Fig. 3. Dynamics of intersubunit orientations

A-B. Comparison of mt-SSU orientations based on common superposition of the mt-LSU. Shifts between equivalent rRNA phosphorus atoms and protein Cα atoms in the different states are color-coded (0-20 Å). A. Intersubunit rotation resembling the ratchet-like mechanism common to all ribosomes. B. Rotation of the small subunit around its long axis. C. Schematic of mitoribosomal conformational changes.

Fig. 4. Distribution of intersubunit bridges

View showing subunit interfaces; residues that form bridges are shown as spheres. Bridges invariant in all classes are shown in purple and dynamic bridges in red. mB7 is specific to class 2 and shown in teal.

Fig. 5. Mitochondria-specific features at the subunit interface

A. h44, mS38 and mS27 coordinate novel bridges with the mt-LSU. B. h44 has been extensively remodeled. The upper half is stabilized by mS38, while the lower half has greater flexibility (the representation of the phosphate backbone is colored and sized by B factor). C. h44 in bacterial ribosomes. D. mS29 mediates mitochondria-specific bridges between the central protuberance and head. E. In monosomes, mS29 is bound to GDP.

Fig. 6. Remodeling of the mRNA channel

A. A wide entrance to the mRNA channel is formed by uS3m and uS5m. B. Overall path taken by mRNA in the human mitoribosome with mS39 located near the channel entrance. C. mRNA emerges through an exit formed by bS1m, bS21m, and mS37.