Chapter 1

Progress toward the Crystal Structure of a Bacterial 30S Ribosomal Subunit

V. Ramakrishnan

V. Ramakrishnan

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84132

Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH England

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Malcolm S. Capel

Malcolm S. Capel

Biology Department, Brookhaven National Laboratory, Upton, NY, 11973

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William M. Clemons Jr.

William M. Clemons Jr.

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84132

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Joanna L. C. May

Joanna L. C. May

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84132

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Brian T. Wimberly

Brian T. Wimberly

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84132

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First published: 27 March 2000

Summary

In 1991, Yonath and coworkers, after nearly a decade of pioneering work on the crystallization of ribosomes, showed that it was possible to obtain diffraction to beyond 3 Å from crystals of the 50S subunit of Haloarcula marismortui. This work marked a milestone in ribosome crystallography, because it established that in principle an atomic-resolution structure of a ribosomal subunit could be obtained. In the meantime, work on whole-ribosome crystallography was also carried out with Thermus thermophilus. The problem of nonisomorphism can be alleviated by the use of multiwavelength anomalous dispersion, in which phase information is obtained by data collection on the same crystal at different wavelengths. Alpha helices of proteins are also visible in the structure, so that it is possible to find and to determine the orientations of proteins of known crystal structure in the map. It is possible to see protein-RNA complexes in many cases. It was possible to determine a fold for it even though the resolution is well below the traditional “atomic” resolution of 3.5 Å required for a new trace because the central domain contains a high density of proteins of previously known crystal structure and well-characterized biochemistry. It is tempting to model much of the ribosome at an intermediate resolution, where one can see double-stranded RNA and recognize known protein structures, or at even-lower resolution, as has been done by others in conjunction with biochemical and electron microscopic data.

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