Extended Data Fig. 1: Ribosome sub-tomogram analysis of Cm-treated M. pneumoniae cells.
From: Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells
a, Slice of a denoised representative cellular cryo-tomogram of M. pneumoniae. Several ribosomes (red boxes), the plasma membrane, and edge of the grid support film are annotated. b-c, The 70S ribosome consensus map (b), and colored by local resolution (c, scale shown on bottom right). d, Fourier Shell Correlation (FSC) curves for the 70S ribosome consensus map, the small (30S) and large (50S) subunits after focused refinements on the 70S ribosome consensus map. e-f, Maps of the small and large subunits after focused refinements on the 70S ribosome consensus map (e), and colored by local resolution (f). g, B factor plots for the dataset processed in the current work (Before M, +Cm, K3; Cm-treated, K3, M) in comparison to our previously published untreated and Cm-treated M. pneumoniae ribosome data (collected with a K2 camera) after M refinement15. h, Comparison of cell thickness distribution for the three datasets described in g. Each dot represents a cell. Red lines indicate mean and standard deviation. Cell thickness for the dataset described in this work is 145 ± 35 nm (n = 137 cells). The thicknesses of 356 and 65 cells are plotted for the previously published data of untreated and Cm-treated datasets15. i, B factor plots for selected tomogram subsets of different cell thickness form the current dataset. The cell number (in brackets), mean thickness and standard deviation values are shown. Analysis of a subset of cells with thickness around 100 nm achieved a B factor lower than 80 Å2. j, Overview of polyamines resolved and modeled in the ribosome structure. k, Two Mg2+ ions coordinated by 23S rRNA nucleotides30. l, Region near the PTC showing rRNA nucleotides and ions. Five coordination bonds for the K+ ion can be mapped37.
