Structure of the CDH1 protein and EC1-2 junction. (a) The full-length E-cadherin protein has 882 amino acid residues in 7 domains. Sites of non-synonymous mutations and deletions are shown with red lines. (b) Red lines and triangles indicate non-synonymous mutations in extracellular cadherin (EC) domains. (c) CDH1 has five EC domains (EC1–EC5, which form a β-barrel structure) and four EC junctions (EC1-2, EC2-3, EC3-4, and EC4-5). The green spheres represent Ca2+ ions. The red and blue spheres represent somatic mutations found in this study and previously reported mutations found in hereditary diffuse-type gastric cancer, respectively. (d, e) CDH1 mutation sites in the EC1-2 junction. In the case of the D221G mutation, oxygen atoms of the aspartic acid side chain, which normally interact with Ca2+, are absent when the aspartic acid residue is replaced with a glycine. In the case of the D257N mutation, the two oxygen atoms of the Asp side chains become one oxygen atom and one nitrogen atom when aspartic acid is replaced with asparagine. In the N256S mutation, the oxygen atom of the asparagine side chain is preserved, but the distance between the oxygen atom and the Ca2+ ion is increased from 2.52 Å to 3.73 Å. All structures were drawn by using PyMOL Molecular Graphics System (v0.99rc6; Schrödinger LLC).