Fig. 1.

Analysis of the folding, hexamerization, and ligand binding of drHerA. A The side and top view of the drHerA-ADP hexamer. Each subunit is labeled and highlighted in distinct colors. In the top view of drHerA, the HAS domains were hidden in order to show the DNA-binding residues (six Arg495 are shown as the surface with blue color) clearly. The size of the drHerA-ADP complex and the diameter of the ring were measured in PyMOL and are labeled. B 2D class averages from cryo-EM showed that the drHerA exists as a hexamer, with or without the addition of ligand/dsDNA. C Details of the drHerA protomer. Upper, the domain arrangement of drHerA. The HAS, RecA-like, and helix-bundle domains are colored magenta, yellow, and marine, respectively. The motifs important for DNA translocation are colored lime green. Lower, a cartoon view of the drHerA protomer. Each domain is colored the same as the domain arrangement. The neighboring protomer is colored white. D The topology diagram of drHerA RecA-like domain. Residues for metal binding, ATP binding, and DNA binding are shown as red, blue, and cyan dots, respectively. Inserted domains/motifs are shown as grey triangles. E The zoom-in view of the ATP catalytic sites. The residues important for ligand and metal binding are shown as sticks and labeled. F Overview of the conformational changes of the ATP catalytic sites between the apo drHerA structure and the drHerA-ADP complex structure. The two structures were superimposed on the RecA-like domain, Chain D. The HerA apo structure is colored white. Arrows indicate directions of the movement of structural elements