Fig. 4: B-subunit/DNA contacts and the conformational plasticity of Top6.
From: Supercoiled DNA recognition and cleavage control in topoisomerase VI
a Examples of H2TH (purple cartoon) and transducer (orange cartoon) domain interactions with DNA (blue cartoon with orange/red stick phosphodiester backbone) in the symmetric, uncleaved state. b Comparison of the five different Top6 holoenzyme reconstructions determined in this paper (WT symmetric: 9O8P/EMD-70232, WT tilt-symmetric: 9O8Z/EMD-70239, WT lopsided: 9O9M/EMD-70259, Top6(A:E342Q) lopsided: 9O7O/EMD-70206, Top6(A:E342Q) cleavage: 9O0G/EMD-49972), shown as thin cartoon models in semitransparent gray cryoEM density maps. The DNA-binding residues of the B subunits are shown as spherical atomic representations and colored and labeled in green or red depending on whether they are close enough to engage DNA in that state. c, d Native agarose gels of negative DNA supercoil relaxation activity comparing the Top6(B:R457A/K460A/H461A) and Top6(B:K471A/K475A) transducer stalk variants, respectively, with the wildtype enzyme. Results are shown from 1 of 2 virtually identical experimental replicates for each panel. Uncropped gel images are provided as a Source Data file.
