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. Author manuscript; available in PMC: 2015 Oct 1.
Published in final edited form as: Nat Struct Mol Biol. 2015 Mar 16;22(4):342–344. doi: 10.1038/nsmb.2992

Figure 1. Electron density maps allow comprehensive modeling of rRNA and ribosomal protein modifications of the 30S subunit.

Figure 1

(a) Spatial distribution of modified nucleotides in the structure of the small ribosomal subunit from T. thermophilus. Here, in Fig. 2 and throughout the text rRNA nucleotides are named according to the E. coli numbering system. Panels (b-i) show unbiased difference Fo-Fc electron density maps for eight types of modifications present in 16S rRNA and ribosomal proteins S12 and S4. Grey mesh shows the Fo-Fc map after refinement with the entire modified nucleotides or amino acid residues omitted (contoured at 2.7-3.0σ). Green mesh shows the Fo-Fc electron density map after refinement with unmodified nucleotides (contoured at 1.5-2.5σ). The modifications shown are: (b) N3-methyluridine 1498, (c) N4,O2’-dimethylcytidine 1402, (d) N2-methylguanosine 1207, (e) N2-dimethylguanosine 966, (f) N7-methylguanosine 527, (g) N6-dimethyladenosine 1519; (h) β-methylthioaspartate of protein S12, (i) 4Fe-4S iron-sulfur cluster of protein S4.