Crystal structure of the 30 s ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 s RNA

• Published in: Journal of molecular biology 2002-02, Vol.316 (3), p.725-768
• Main Authors: Brodersen, Ditlev E., Clemons, William M., Carter, Andrew P., Wimberly, Brian T., Ramakrishnan, V.
• Format: Article
• Language: English
• Subjects: 16 S RNA; 30 S; Amino Acid Sequence; assembly; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Base Sequence; Binding Sites; Crystallography, X-Ray; Microscopy, Electron; Models, Molecular; Molecular Sequence Data; Neutrons; Nucleic Acid Conformation; Protein Binding; Protein Structure, Secondary; Protein Structure, Tertiary; Protein Subunits; protein-RNA interactions; Ribosomal Proteins - chemistry; Ribosomal Proteins - metabolism; ribosome; Ribosomes - chemistry; Ribosomes - genetics; Ribosomes - metabolism; RNA, Ribosomal, 16S - chemistry; RNA, Ribosomal, 16S - genetics; RNA, Ribosomal, 16S - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - metabolism; Scattering, Radiation; Sequence Alignment; Thermus thermophilus; Thermus thermophilus - chemistry; Thermus thermophilus - genetics
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.2001.5359

We present a detailed analysis of the protein structures in the 30 S ribosomal subunit from Thermus thermophilus, and their interactions with 16 S RNA based on a crystal structure at 3.05 Å resolution. With 20 different polypeptide chains, the 30 S subunit adds significantly to our data base of RNA structure and protein-RNA interactions. In addition to globular domains, many of the proteins have long, extended regions, either in the termini or in internal loops, which make extensive contact to the RNA component and are involved in stabilizing RNA tertiary structure. Many ribosomal proteins share similar α+β sandwich folds, but we show that the topology of this domain varies considerably, as do the ways in which the proteins interact with RNA. Analysis of the protein-RNA interactions in the context of ribosomal assembly shows that the primary binders are globular proteins that bind at RNA multihelix junctions, whereas proteins with long extensions assemble later. We attempt to correlate the structure with a large body of biochemical and genetic data on the 30 S subunit.