Extended Data Fig. 3: Superposition of the cryo-EM map with the models of various features within the Arabidopsis PhyA dimer.

The map is shown in grey mesh whereas the 3D models of the motifs/residues are shown in cartoons/sticks and colored as in Fig. 1e. Panels a-c include PΦB (red sticks) to highlight proximity to the chromophore. Key residues are indicated. a, Knot lasso extending from the GAF domain to encircle the N-terminal extension (NTE) just upstream of the nPAS domain. b, Residues 69–81 comprising part of the NTE near the knot lasso that reaches near the chromophore. c, Orthogonal views of the hairpin extending from the PHY domain to contact the GAF domain near the chromophore. d, The modulator loop extending from between the PAS1 and PAS2 domains to interact with the PHY domain of its own protomer. e, The paired DHp domains within the HKRD. Helices α1 and α2 are indicated. The cruciate feature within helix α1 is located by the brackets. Residue 905 (R905), which is normally occupied by a histidine in transmitter histidine kinases, is highlighted by the red oval. f, Closeup views of the connections between the PAS2 domain of protomer B and the nPAS and GAF domains of protomer A within the dimer. g, Structural prediction of the PAS1 fold by TrRosetta (left) and congruence of this prediction (grey) with the cryo-EM models of the PAS2 (center) and nPAS domains from PhyA (right) shown in color. The N- and C-terminal ends are indicated. For panels (e) and (f), the peptide backbone is shown in cartoon, whereas the amino acid side chains are in sticks. The prime designations identify residues from the B protomer.