Cryo-EM structure of prothrombin bound to fVa and fXa. Molecular surface representation of the ternary complex of prothrombin fVa and fXa. The complex in Figure 1B is shown in different orientations obtained by 90° rotation of the reference view (B) as indicated by arrows. The constitutive domains of prothrombin, fVa and fXa are rendered in the same colors as in Figure 1B. Prothrombin engages prothrombinase through the protease domain (B,D-E) that binds to the A2 domain of fVa (B-D) and the protease domain of fXa (A-C). The protease domain of fXa is in close contact with the A2 domain of fVa (B,E). Labeled are the sites of prothrombin activation by prothrombinase at R271 (B-C,E) and R320, which is visible only looking up from the plane of the membrane (A) as it penetrates the active site of fXa. The preferred site of prothrombin activation in the absence of fVa, R155, is located on the side of prothrombin opposite to that facing fXa (D). The 672 to 691 region of the A2 domain of fVa changes conformation in the complex relative to the free form³⁵ (C,E) and closes like a lid on the protease domain of fXa while making direct contacts with R271 of prothrombin (C,E; see also Figure 5 for details).