Three-dimensional placement of the conserved 530 loop of 16 S rRNA and of its neighboring components in the 30 S subunit

The small ribosomal subunit from Thermus thermophilus at 4.5 Å resolution: Pattern fittings and the identification of a functional site

“…The non-oligomer-bound mercury atoms of the TAMM molecule were masked to avoid the attachment of the oligomers to undesired locations as described (11). The oligomer presented in these studies was (AGAAAG-GAGGTGATC), to which a tail of A(thio-dG) 3 was added.…”

“…It contains 21 proteins and an RNA chain (16S) of Ϸ1,500 nucleotides. Significant conformational variability of 30S particles has been observed by cryoelectron microscopy studies (1,2), by surface probing (3), and by monitoring the ribosomal activity (4).…”

“…Consequently, the structure determination proceeds by step-wise approach, progressing from low to higher resolution. Furthermore, most of the interpretations of the currently available electron density maps hinge on models accommodating noncrystallographic structural information (3,4,(12)(13)(14)(15)(16)(17)(18)(19) and exploiting known structures of RNA and of isolated ribosomal proteins. Considerable uncertainties are associated with placements of structures determined at high resolution in medium resolution maps.…”

Large-Scale Motions within Ribosomal 50S Subunits as Demonstrated Using Photolabile Oligonucleotides

“…Since this seminal article, photoinduced crosslinking and the related approach of photoaffinity labeling have been used extensively to explore binding sites of a large number of biological macromolecules (2), particularly those deemed too large for direct structure elucidation. In recent years we have used photoinduced crosslinking to examine ribosome structure (3)(4)(5)(6). In our studies radioactive, photolabile derivatives of oligonucleotides (PHONTs), 2 having sequences complementary to rRNA sequences, are bound to their targeted sequences in intact ribosomes or ribosomal subunits, and, on photolysis, incorporate into ribosomal components that can subsequently be identified.…”

“…In our studies radioactive, photolabile derivatives of oligonucleotides (PHONTs), 2 having sequences complementary to rRNA sequences, are bound to their targeted sequences in intact ribosomes or ribosomal subunits, and, on photolysis, incorporate into ribosomal components that can subsequently be identified. This work initially had as a goal the generation of constraints that, in concert with other kinds of information (footprinting and other chemical modification approaches, immunoelectron microscopy, image reconstruction of electron micrographs), could be used to construct three-dimensional models of ribosome structure (6)(7)(8)(9). This goal has largely been rendered obsolete by the publication in the last 2 years of high resolution X-ray structures of 30S and 50S subunits of bacterial ribosomes, and somewhat lower resolution structures of 70S ribosomes, which provide an exquisitely detailed picture of how various elements (proteins, RNA helices) fit together in forming this fascinating and important macromolecular structure (10)(11)(12)(13)(14)(15).…”