Figure 3
From: Red light-induced structure changes in phytochrome A from Pisum sativum
Selection of the most probable molecular shape of the Pr dimer (a, b) and Pfr dimer (c, d). In panels (a, c), 560 models from independent ab initio calculations are plotted on the plane spanned by the first and second eigenvectors from PCA. Through K-means clustering, the models were classified into 10 groups designated I-X. The number of the Pr models classified into groups I-X are 2, 75, 43, 59, 73, 77, 142, 10, 70, and 9, respectively. On the other hand, those of the Pfr models in groups I-X are 45, 23, 38, 23, 116, 84, 150, 41, 79, and 15, respectively. The molecular shape of each group was obtained by averaging the DR models after superimposition on a reference structure. The averaged shape for each group was illustrated using UCSF Chimera57,58. Panels (b, d) show averaged shapes for group II of Pr and group I of Pfr, respectively. The representing shapes are shown as mesh models with arrows and symbols representing the two-fold symmetry axes. In panel (b), the four-leaf shaped model (dashed lines) in the early stage of our SAXS study38 is superimposed. (e) Superimposition of averaged molecular shapes of Pr (red mesh) and Pfr (blue).
