Cryo-EM structure of the FVa-APC complex. The cryo-EM structure of the FVa-APC complex solved at atomic (3.15 Å) resolution reveals the A1-A2-A3-C1-C2 assembly of FVa and the Gla-EGF1-EGF2-PD assembly of APC. (A) Electron density map and atomic model of the complex showing the unsharpened consensus map (gray, EMD-48439) with embedded model (PDB 9MOV) as a cartoon representation (top). Constitutive domains are colored in yellow (A1), green (A2), cyan (A3), brown (C1), purple (C2) for FVa, red (PD), and blue (Gla, EGF1, and EGF2) for APC. GSFSC for the unsharpened map (bottom). (B) Electron density map from 3D flexible refinement showing the DeepEMhancer sharpened map (EMD-48481) of the FVa-APC complex with domains (top) colored as in panel A. Sites of glycosylation appearing as bulges in the unsharpened map in panel A are colored in orange. GSFSC for the sharpened map (bottom). (C) Representative reference model-free 2D class averages. GSFSC, gold-standard Fourier shell correlation.