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

Nature. 1999 Aug 26;400(6747):841-7. doi: 10.1038/23641.

Abstract

We have calculated at 5.0 A 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Archaeal Proteins / chemistry
  • Crystallography, X-Ray
  • Haloarcula marismortui / chemistry
  • Haloarcula marismortui / ultrastructure
  • Nucleic Acid Conformation
  • Protein Conformation
  • RNA, Archaeal / chemistry
  • RNA, Ribosomal / chemistry*
  • Ribosomal Proteins / chemistry*
  • Ribosomes / chemistry*
  • Ribosomes / ultrastructure

Substances

  • Archaeal Proteins
  • RNA, Archaeal
  • RNA, Ribosomal
  • Ribosomal Proteins
  • ribosomal protein L11
  • ribosomal protein L14
  • ribosomal protein L6

Associated data

  • PDB/IC04