FIGURE 6.

Fitting of subunit C and H crystal structures into the yeast V-ATPase three-dimensional model. A, overlay of the high (green) and low (yellow) conformers of subunit C (PDB 1u7l; Ref. 42). As can be seen, the foot domains (C_ft) match well, whereas the position of the head domains (C_hd) varies, indicating some flexibility of the two domains. Coordinates of the low-resolution conformer were kindly provided by Dr. Nathan Nelson. The sites from where cross-linking to EG has been observed (34) are in red spacefill. B and C, fitting of both subunit C conformers into the V-ATPase three-dimensional model reveals a better fit for the low-resolution conformer. D, crystal structure of subunit H (PDB 1ho8; Ref. 43) showing an N-terminal domain (H_nt) and a C-terminal domain (H_ct). Conserved residues are in white spacefill. Residues from where cross-links to subunits E, B, and F have been observed (54) are in red, blue, and magenta spacefill, respectively. E, fitting of the crystal structure of subunit H into the V-ATPase three-dimensional model. In this orientation, the sites cross-linking to B and F are on the outside. The H_ct domain was therefore fitted separately (see panel F) in accordance with the independent behavior of the two domains as reported for the yeast enzyme (55).