The PDB and the ribosome

Abstract

This essay, which was written to commemorate the 50th anniversary of the Protein Data Bank, opens with some comments about the intentions of the scientists who pressed for its establishment and the nature of services it provides. It includes a brief account of the events that resulted in the determination of the crystal structure of the large ribosomal subunit from Haloarcula marismortui. The magnitude of the challenge the first ribosome crystal structures posed for the PDB is commented upon, and in the description of subsequent developments in the ribosome structure field that follows, it is pointed out that cryo-EM has replaced X-ray crystallography as the method of choice for investigating ribosome structure.

Keywords: PDB; cryo-EM; crystallography; model; ribosome; structure.

Figure 1

The binding sites of a W₁₁cluster compound in the exit tunnel of the Hma LRS.A, a stereo pair of the large ribosomal subunit with the part proximal to the viewer cut away to reveal the four sites where the W₁₁ compound binds. B, a close-up of the interior of the exit tunnel showing the wall of its lumen and the four W₁₁ sites. Reproduced from (28) with the permission of the publisher.

Figure 2

A space-filling model of the subunit interface surface of the Hma LRS. Nonhydrogen atoms are shown as van der Waals spheres. Protein atoms are blue. Atoms belonging to nucleotide bases are gray. Backbone atoms belonging to 23S rRNA are brown, and those associated with 5S rRNA are purple. The atoms of a peptidyl transferase substrate analogue bound in peptidyl transferase center are green. This image was prepared for the author by Professor Poul Nissen.

Figure 3

Some proteins in the Hma LRS that have tails. Globular domains are green. Tails are red. Purple spheres are Zn²⁺ ions. Proteins are named following the rules provided in (52). (Note: Protein eL42 is called L44e in many publications) (Redrawn from (19)).