Fig. 3: Structural heterogeneity of pyrenoid Rubisco.

a–c D4-symmetric maps of four classes out of ten (Supplementary Fig. 2), which were refined to the highest resolution, along with their proportion in the “good” subtomogram dataset (Supplementary Table 3). b–g Difference maps showing major variations in density between classes. Positive densities resulting from the subtraction of one map from another as indicated in the panels are colored dark blue and negative densities are colored green. Difference maps between classes were calculated from confidence maps binarized at 1% false discovery rate threshold, Gaussian filtered, and presented at 10 standard deviations (SDs) contour level. For orientation, the difference maps are overlayed on the class 12 low-passed filtered map and fitted MDFF model (Fig. 2a). Large subunits, small subunits and active site residues are colored grey, orange, and dark red, respectively.