FIG. 2.

Sections of the X-ray map of native HRV14 and of the reconstructed cryo-EM map of the nearly empty HRV14 reduced in size by 4% for comparison. The two-, three-, and five-fold axes are indicated as appropriate. Asterisks and closed arrowheads indicate the positions of additional density inside the empty capsid on the three- and fivefold axes, respectively. (A and B) Fifteen-Å-thick sections of the scaled HRV14 empty capsid (gold) and the native HRV14 capsid simulated with (red) and without (blue) VP4 and the N terminus of VP1. Open arrowheads indicate the positions of VP4 and the N terminus of VP1. In the absence of these chains, the two structures match much better on the inner surface (B). (C and D) Central sections of the X-ray map of native HRV14 minus VP4 and the N terminus of VP1 (C) and of the reconstructed cryo-EM map of the size-matched empty HRV14 (D). (E, F, and G) Sections of the size-matched HRV14 nearly empty capsid (pink) and the native HRV14 capsid simulated without VP4 and the N terminus of VP1 (dark blue). C_α backbones of the known X-ray structures of VP1, VP2, VP3, and VP4 are depicted in blue, green, red, and yellow, respectively, in their positions in the native capsid. In panels E and F, the VP4 molecules are seen to be attached to the additional density on the fivefold axis. Panel F demonstrates missing density inside the empty capsid on the twofold axis compared with the density in the native capsid. The bubble of low density on the pseudo threefold axis is unchanged, and the pocket in VP1 is visible in the native capsid but is not visible in the empty capsid in this section as it is displaced and smaller. (G) The N terminus of VP2 is seen to point into the additional density on the threefold axis, which is sufficient to accommodate the seven disordered N-terminal residues of VP2.