Fig. 2: Structural basis for Ca²⁺ binding.

a Side view of hSPCA1 in the CaE1-ATP state. N and P domains are colored forest green and peru, respectively. A domain and TM1–TM2 are hidden for a clearer view. TM3 is colored hot pink. TM4 and TM6 are colored orange-red. TM5 and TM7–TM10 are medium purple. Ca²⁺ is shown as the lime sphere. The Ca²⁺ density (contoured at 15 σ) is shown as black mesh. b Atomic models and cryo-EM densities of Ca²⁺ and Ca²⁺-binding site of hSPCA1 in the CaE1-ATP state. Ca²⁺-binding residues are shown as the cyan sticks and Ca²⁺ is shown as the lime sphere. The densities are shown as black mesh, contoured at 15 σ. The interactions between residues and Ca²⁺ are shown by magenta dashed lines. c The stability of the Ca²⁺ substrate in the binding site observed in a 1-µs explicit solvent all-atom MD simulation. It shows the trajectory of the distance between the Ca²⁺ ion and the center of the lipid bilayer. d The two Ca²⁺-binding sites of hSERCA2 in the CaE1-ATP state (PDB: 6LLE). Ca²⁺ ions are shown as dark gray spheres. Ca²⁺-binding residues are shown as sticks. The magenta dashed lines represent the metal coordination bonds. e Comparison of the Ca²⁺-binding sites between hSPCA1 and hSERCA2 in the CaE1-ATP state. Site I and site II counterpart residues in hSPCA1 are shown as cyan sticks. Dark gray sticks are the Ca²⁺-binding site I residues in hSERCA2. The black dashed lines show the distance between the Ca²⁺-binding oxygen atoms from Asp799 and Glu907 in hSERCA2 and the distance between the oxygen atoms from Asp742 and Asp819 in hSPCA1, respectively. f Sequence alignment of hSPCA1 and hSERCA2. Black asterisks indicate residues contributing to Ca²⁺-binding site I. Blue asterisks indicate residues contributing to Ca²⁺-binding site II. The red asterisk indicates the residue contributing to both sites I and II.