SS- and X-dimer structures consisting of full-length ectodomains (EC1 to EC5) of E-cadherin were modeled using BIOVIA Discovery Studio 2017 R2 (Dassault Systèmes) by fitting the EC1–EC2 parts of the full-length ectodomains (PDB ID code: 3Q2V chain A) (25 (link)) to both sides of the SS- and X-dimers formed by EC1–EC2 (PDB ID codes: 2QVF and 3LNH) (10 (link)), respectively. Based on these full-length ectodomain structures, pseudo-AFM images of the SS- and X-dimers (Fig. 2B and D and SI Appendix, Fig. S7A and D) were produced using the laboratory-made analysis software FalconViewer based on Igor Pro-8 (WaveMetrics) by setting the paraboloid-shaped tip of the AFM probe with a tip radius of 0.5 nm. The images were processed using a low-pass filter with a cutoff frequency of 2 nm. A modified model structure of the X-dimer (shown in SI Appendix, Fig. S7E) was created to orient the EC3–EC5 region more flatly on the substrate, by rotating the dihedral angle φ of Lys212 (in the EC2–EC3 linker) to 180°. Models of the ectodomains and dimers (Fig. 6) were produced using Blender 2.93.5 (Blender Foundation). The pseudo-AFM images obtained in this study were deposited in the Mendeley Data Repository (53 ).