PCA and ANM calculations for rhodopsin. (A) PCA analysis of 16 x-ray structures. On the left, backbone conformations are optimally superimposed. On the right, the loci of the examined structures in the subspace spanned by the two top-ranking PCA modes (p⁽¹⁾ and p⁽²⁾) are shown. PCA mode 1 correctly clusters the inactive (rhodopsin) and (putative) activated (opsin) structures into two separate groups. Mode 2 further differentiates the structures in the cluster of inactive rhodopsins. (B) Superimposition of experimentally determined rhodopsin (PDB accession no. 2GZM) and opsin (PDB accession no. 3CAP) conformers viewed from the side (top) and cytoplasmic region (bottom). (C) Rhodopsin structure generated by reconfiguring the opsin along the first PCA mode, viewed from the same two perspectives. (D) Rhodopsin conformation predicted by deforming opsin along the 20 lowest frequency ANM modes. A cutoff distance of 8 Å was adopted in the ANM for defining inter-residue contacts.