Structure and transport mechanism of the human calcium pump SPCA1

Secretory-pathway Ca²⁺-ATPases (SPCAs) play critical roles in maintaining Ca²⁺ homeostasis, but the exact mechanism of SPCAs-mediated Ca²⁺ transport remains unclear. Here, we determined six cryo-electron microscopy (cryo-EM) structures of human SPCA1 (hSPCA1) in a series of intermediate states, revealing a near-complete conformational cycle. With the aid of molecular dynamics simulations, these structures offer a clear structural basis for Ca²⁺ entry and release in hSPCA1. We found that hSPCA1 undergoes unique conformational changes during ATP binding and phosphorylation compared to other well-studied P-type II ATPases. In addition, we observed a conformational distortion of the Ca²⁺-binding site induced by the separation of transmembrane helices 4L and 6, unveiling a distinct Ca²⁺ release mechanism. Particularly, we determined a structure of the long-sought CaE2P state of P-type IIA ATPases, providing valuable insights into the Ca²⁺ transport cycle. Together, these findings enhance our understanding of Ca²⁺ transport by hSPCA1 and broaden our knowledge of P-type ATPases.