Fig. 3.

Fitting of atomic structure of RRF into the cryo-EM density. (a) Stereo-view representation of the fitting of the x-ray structure of T. maritima RRF (domain I, pink; and domain II, violet) into the cryo-EM density (semitransparent red). In most part, the x-ray structure of RRF is embedded within the cryo-EM density, recognizable by altered hues of color for the two RRF domains (reddish pink for domain I, magenta for domain II), whereas very small portions of the x-ray structure that stick out of the cryo-EM density are visible in their original (pink or violet) colors. The cryo-EM density of RRF is shown at a lower threshold value as compared to the value used in Figs. 1 and 2. (b) Same as a, but shown from the intersubunit space side, with L7/L12 stalk facing the viewer. (c) Alternative fitting of RRF atomic structure (gray) into the cryo-EM map shown from the same view as in b. In this fitting, domain II of RRF is oriented into a weaker mass of density (semitransparent green, see text), toward the L7/L12 stalk-base region. This fitting yields a significantly lower cross-correlation value (0.51 vs. 0.77 for the fitting shown in a and b). For the purpose of comparison, only C_α backbones of RRF x-ray structure are shown in b and c. The orientations of the 70S ribosome (semitransparent surfaces), with RRF density (red), are shown as thumbnails on the lower right. All of the landmarks are the same as in Fig. 2.