Structure and transport mechanism of the human calcium pump SPCA1

Abstract Secretory-pathway Ca 2+ -ATPases (SPCAs) play critical roles in maintaining Ca 2+ homeostasis, but the exact mechanism of SPCAs-mediated Ca 2+ 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 Ca 2+ 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 Ca 2+ -binding site induced by the separation of transmembrane helices 4L and 6, unveiling a distinct Ca 2+ release mechanism. Particularly, we determined a structure of the long-sought CaE2P state of P-type IIA ATPases, providing valuable insights into the Ca 2+ transport cycle. Together, these findings enhance our understanding of Ca 2+ transport by hSPCA1 and broaden our knowledge of P-type ATPases.