Figure 2.

SVD analysis of RB69 DNA polymerase structures. (A and B), the second and third components U’₂ and U’₃, also known as left singular vectors (‘Materials and Methods’ section). See also Supplementary Figure S1 for more details on SVD results. The motion of the fingers is decoupled from those of exo and thumb domains. These motions are separated into two independent components U’₂ and U’₃. The domains are divided by grids and marked on the matrix diagonals. The motions of exo and thumb are highly concerted, since the red and blue bands of these domains are equally strong in a same component (B). (C, D, E and F), the coefficient sets in the first four dimensions, also known as right singular vectors. Each dot represents a polymerase structure. Its distance matrix could be approximately reconstructed as a linear combination c₁U₁ + c₂U₂ + c₃U₃ + c₄U₄. That is to say, two dots close to each other in the conformational space indicate two similar linear combinations thus represent two similar structures. Two dots far apart represent two distinct structures. The distance between two dots is equivalent to the rmsd value between two structures. The down→up arrow indicates that β-hairpin movement is possible among all structures (Supplementary Figure S1d). The color of each dot indicates the type of ligand bound opposite the template base in the polymerase active site. A dash (-) indicates no ligand; and a question mark (?) indicates that a ligand could be bound but not observed in the structure. See Supplementary Table S1 for all types of ligands. Sixty-two open structures stretch out horizontally at c′₂ ≈ 2, but 96 closed structures share constant values of c′₂ ≈ −1.4 and c′₃ ≈ −0.4. The tight cluster of closed structures is also magnified in (F). The other 11 structures with missing parts in the fingers domain are omitted for clarity. The closed→open and near→far arrows indicate discrete and continuous conformational changes, respectively. See also Supplementary Movie S1 for the continuous motion from near to far conformation. (G) Singular values with the top four highlighted in green.