Cryo-EM structures of lipid nanodisc-bound prothrombinase (top) and prothrombinase in a ternary complex with prothrombin (bottom). Top, FVa is represented in gray, with the A1, A2, A3, C1, and C2 domains labeled. FXa is shown in pink with the Gla, EGF1, and protease domains labeled, forming connections with the FVa A2, A3, and C1 domains. The protease domain of FXa is held in place with an FVa A2 domain “lid” (residues 672-691, shown in blue). The lipid nanodisc is modeled below to illustrate how these domains bind membrane surfaces. Bottom, prothrombinase (FVa/FXa) bound to prothrombin in its “closed” form. Prothrombin is shown in orange, with the Gla and Kringle (K1 and K2) domains labeled, which makes a small contact with the FVa A2 domain 696 to 702 loop (green). R320 projects toward the specificity site adjacent to the active site of FXa (pink). R271 sits above the 696 to 702 loop. EGF1, epidermal growth factor-like domain 1; ND, lipid nanodisc; PT, prothrombin.