Figure 3.

IsPadC^PG dimer^E/E structure. A, crystallographic model of the IsPadC^PG dimer^E/E. Three of the eight protomers present in the asymmetric unit are shown to visualize the distinct dimer interfaces observed. NTS region, PAS, and GAF domains are colored gray, purple, and blue, respectively. 15E BV is represented as sticks and colored dark red. B, close-up view of the Pfr-like BV conformation. The 2F_o − F_c electron density map contoured at 1σ around the chromophore is shown as gray mesh. Important residues defining the Pfr environment are shown as stick representation. C, structural superposition of the IsPadC^Reg2 Pfr state (orange, PDB code 6et7 (9)) to the IsPadC^PG dimer^E/E structure based on the PAS–GAF core (residues 1–312, RMSD = 0.36 Å over 267 Cα atoms). The structural feature indicated with LXP corresponds to the start of the LXPRXSF motif of the PHY-tongue. L, Leu-186 in IsPadC^PG and Leu-446 in IsPadC; X, Phe-187 in IsPadC^PG and Gly-465 in IsPadC; P, Thr-188 in IsPadC^PG and Pro-466 in IsPadC. D, changes in conformational dynamics upon IsPadC^PG dimerization during red light illumination evaluated by HDX-MS. The structure is colored according to the observed changes in relative deuterium incorporation (ΔD_rel) between the IsPadC^PG dimer^E/E and the IsPadC^PG monomer^Z dark state after 15 min of deuteration. The changes in ΔD_rel are indicated by the scale on the left side with blue corresponding to reduced deuterium incorporation and red reflecting increased exchange of amide protons. 15E BV is represented as sticks and colored dark red.