Virtuelle (Nano) Welten: PDB Molecule of the Month 10: Ribosome

The Large Subunit

The structure of the large subunit is available in PDB entries 1ffk. The large subunit contains the active site of the ribosome: the site that creates the new peptide bonds when proteins are synthesized. In this view, the messenger RNA would run horizontally in the groove across the middle. This structure, along with several other structures with inhibitors bound, provide strong evidence that the ribosome is a ribozyme. Enzymes typically use amino acids to catalyze chemical reactions, but the ribosome appears to use an adenine RNA nucleotide to perform its synthetic task. This adenine is colored green in the figure (we'll look at this more closely later).

The large subunit is composed of two RNA strands: a long one colored orange and a shorter one colored yellow. Dozens of proteins bind on the surface of the ribosome. Many have long, snaky tails that extend into the body of the ribosome, gluing the RNA strands into their proper shape. Several of the proteins were not seen in this crystallographic structure, perhaps because they are too flexible. Approximate shapes for these proteins, which form two prominent stalks commonly used as landmarks in electron micrographs, are indicated here in light blue.

To download an animated movie of this subunit, click on the molecule.