3-D map of the (PA₆₃)₇–(LF)₃ complex and its atomic interpretation. (A–D) The map of (PA₆₃)₇–(LF)₃ obtained by cryo-EM single-particle reconstruction at 16-Å resolution is shown in isosurface representation. (A) Side view showing the upside down L shape of LF molecules with a gap of ∼30 Å tall (blue oval) between the surface of PA and the LF_C domains. (B) Side view, rotated about a vertical axis by ∼100° counterclockwise compared with A, showing the major intermolecular LF_C–LF_N interaction within the complex (circled in red here and in C), and a minor contact visible at lower contour levels (red arrows here and in C). (C) Top-down view of the complex showing three LF molecules, each in unique environment (named from above ¹LF, ²LF, and ³LF; see F), Note the “gap” (marked by black arrow) caused by the symmetry mismatch, the major intermolecular LF_C–LF_N (circled in red), and the minor contact visible at a lower contour level (red arrows). (D) View from below reveals the strong sevenfold symmetry of (PA₆₃)₇, which was not imposed during refinement. (E and F) Atomic models derived by rigid-body docking of component crystal structures into the EM map. The view in E looks directly into the gap, which overlooks the orphan PA₆₃ moiety and is a rotation of A by 100° clockwise. The view in F is the same as C. The three LF molecules fit their respective densities with CC > 0.98, whereas the junctions between the LF molecules and their cognate PA molecule have CC > 0.97. Bars, 50 Å.