Figure 3

The related analyses of AFM images. (a) Height distribution of the AFM image Fig. 2a (n = 262,144). The peak-to-peak is 2.02 nm. (b) Ribbon style view of crystallography structural model of E-cadherin extracellular domains created with PyMOL. The EC5 of one side was not resolved (PDB ID: 3Q2V²⁸) and is represented by a dotted line. Calcium ions are shown as red spheres. (c) Crystallography structural model (PDB ID: 5JII⁴⁴) of IgG-Fc domain created with PyMOL. Hinge regions are not included in the model. The hinge region follows the N-terminal, residue 237⁵³ (red triangular), which appears in this crystallography structural model. Examination with PyMOL revealed that the size of the Fc domain was 6.7 nm in length, 6.3 nm in width, and 3.6 nm in height. The three-dimensional structure is shown in movie in Supplementary Video S2. (d) Schematic illustration of Fc molecular model. The CH2CH3 chains are bent and in a skewed position. EC domains are connected to Fc domains comprising CH2, CH3 and hinge regions via linkers. Hinge regions are shown as yellow line. Linkers are shown as violet circle. Brown lines represent disulfide bonds. Because residue 237 is located on the inner periphery of the skewed U-shaped Fc domain, it is presumed the hinge and linker region between EC5 domain and CH2 is located in this neighborhood. (e) Height analysis of Fc domains. The distribution was constructed by using the height data obtained from locations which are considered to correspond to the Fc domain of the E-cad-Fc in Fig. 2a. The median and variance for the first peak were 4.1 nm ± 0.66, while those for the second peak were 5.5 nm ± 0.42 by Gaussian fitting (n = 148). (f) The tilted Fc domain “lying down” model.