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.
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We thank E. Freeborn for biochemical support; R. Sweet for helping us with data collection at the National Synchrotron Light Source; and I.Tanaka, M. Garber and S. Al-Karadaghi for providing coordinates before publication. This investigation was supported by grants from NIH to T.A.S. and P.B.M. N.B. was a Damon Runyon-Walter Winchell Postdoctoral Fellow during part of this study, and P.N. is supported by the Danish Research Council. The coordinates of all identified RNA and protein structures have been deposited in the protein data bank with accession number IC04.
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Ban, N., Nissen, P., Hansen, J. et al. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature 400, 841–847 (1999). https://doi.org/10.1038/23641
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