PDBsum entry 2ftc

Ribosome

PDB id: 2ftc

Contents

Protein chains

189 a.a.*

136 a.a.*

211 a.a.*

175 a.a.*

137 a.a.*

145 a.a.*

148 a.a.*

118 a.a.*

116 a.a.*

98 a.a.*

118 a.a.*

110 a.a.*

96 a.a.*

69 a.a.*

52 a.a.*

38 a.a.*

DNA/RNA

* C-alpha coords only

References listed in PDB file

Key reference

Title

A structural model for the large subunit of the mammalian mitochondrial ribosome.

Authors

J.A.Mears, M.R.Sharma, R.R.Gutell, A.S.Mccook, P.E.Richardson, T.R.Caulfield, R.K.Agrawal, S.C.Harvey.

Ref.

J Mol Biol, 2006, 358, 193-212. [DOI no: 10.1016/j.jmb.2006.01.094]

PubMed id

16510155

Abstract

Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different species. The most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. The RNA component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. Until recently, it was unclear how these changes affect the 3D structure of the mitoribosome. Here, we present a structural model of the large subunit of the mammalian mitoribosome developed by combining molecular modeling techniques with cryo-electron microscopic data at 12.1A resolution. The model contains 93% of the mitochondrial rRNA sequence and 16 mitochondrial ribosomal proteins in the large subunit of the mitoribosome. Despite the smaller mitochondrial rRNA, the spatial positions of RNA domains known to be involved directly in protein synthesis are essentially the same as in bacterial and archaeal ribosomes. However, the dramatic reduction in rRNA content necessitates evolution of unique structural features to maintain connectivity between RNA domains. The smaller rRNA sequence also limits the likelihood of tRNA binding at the E-site of the mitoribosome, and correlates with the reduced size of D-loops and T-loops in some animal mitochondrial tRNAs, suggesting co-evolution of mitochondrial rRNA and tRNA structures.

Figure 5.
Figure 5. Three-dimensional model for the mitochondrial 16 S rRNA. (a) The 16 S rRNA is represented from the interface and solvent-accessible sides of the structure and colored by domain (I, purple; II, dark blue; III, orange; IV, green; V, red; and VI, yellow). (b) The model RNA fit to EM density that is attributable to RNA,13 except for the tip of a domain V helix that contacts the L1 protein. However, the model of the extended rRNA segment fits into the complete LSU map (also see Figure 4(b)). Coloring is the same as in (a).

Figure 7.
Figure 7. Stereo-view representation of the 3D model of the 39 S subunit of the mitochondrial ribosome. (a) The interface view of the subunit shows that the conserved interface of the mitochondrial ribosome is still dominated by rRNA structure (colored as in Figure 5). (b) The homologous MRPs (grey) are located predominantly towards the solvent-accessible side of the particle. Upper and lower panels in both sections show the modeled structure (rRNA and proteins), and its fitting into the cryo-EM map,13 respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 193-212) copyright 2006.