Comparison of the EM map of intact αIIbβ3 embedded in a nanodisc with the crystal structure of the recombinant αIIbβ3 ectodomain. (A) The headpiece in the ectodomain crystal structure (ribbon diagram; PDB: 3FCS) compared with correlation-based docking of headpiece domains into the EM map. Note that the αIIbβ3 headpiece in the 3D reconstruction points away from the membrane and has a more compact conformation than the recombinant ectodomain. (B-C) The overall conformations of the leg domains of αIIb (blue) (B) and β3 (red) (C) in the EM map compared with the crystal structure (ribbon diagram; PDB: 3FCS) displayed by matching the αIIb thigh and β3 hybrid domains, respectively. Note that the αIIb and β3 lower legs in the 3D reconstruction are not adjacent, parallel, and straight as in the crystal structure. Instead, the αIIb calf-1 and calf-2 domains are bent and rotated and the β3 I-EGF 2 to 4 domains are freely coiled. (D) The structure of the calf-2 domain superimposed on the docked calf-2 domain. The disulfide-linked β-tail in the crystal structure (ribbon diagram; PDB: 3FCS) and the β-tail docked in the map are displayed. The distances between the ends of the structured residues in the calf-2 and β-tail domains (αIIb:G954 [blue sphere]; β3:C687 [red sphere]) were measured in the crystal structure (1 = 19.6 Å) and in the fitted structure (2 = 11.7 Å).