Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit

Nenad Ban, Poul Nissen, Jeffrey Hansen, Malcolm Capel, Peter B. Moore and Thomas A. Steitz
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Nenad Ban: Departments of Molecular Biophysics & Biochemistry Yale University
Poul Nissen: Departments of Molecular Biophysics & Biochemistry Yale University
Jeffrey Hansen: Departments of Molecular Biophysics & Biochemistry Yale University
Malcolm Capel: Brookhaven National Laboratory
Peter B. Moore: Yale University
Thomas A. Steitz: Departments of Molecular Biophysics & Biochemistry Yale University

Nature, 1999, vol. 400, issue 6747, 841-847

Abstract: Abstract We have calculated at 5.0 Å resolution an electron-density map of the large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modification procedures. More than 300 base pairs of A-form RNA duplex have been fitted into this map, as have regions of non-A-form duplex, single-stranded segments and tetraloops. The long rods of RNA crisscrossing the subunit arise from the stacking of short, separate double helices, not all of which are A-form, and in many places proteins crosslink two or more of these rods. The polypeptide exit channel was marked by tungsten cluster compounds bound in one heavy-atom-derivatized crystal. We have determined the structure of the translation-factor-binding centre by fitting the crystal structures of the ribosomal proteins L6, L11 and L14, the sarcin–ricin loop RNA, and the RNA sequence that binds L11 into the electron density. We can position either elongation factor G or elongation factor Tu complexed with an aminoacylated transfer RNA and GTP onto the factor-binding centre in a manner that is consistent with results from biochemical and electron microscopy studies.

Date: 1999
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DOI: 10.1038/23641

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