Fig. 7: Cryo-EM structure of the NanR-dimer3/DNA hetero-complex.
From: Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism
a 2D class averages showing three possible NanR dimers bound to DNA in projection (white arrow). b Density map for the NanR-dimer3/DNA hetero-complex. c Three NanR dimers and a DNA duplex were fitted using a rigid body method. Two NanR dimers are clearly visible within the density (gray isosurface) at each end of the DNA, while the middle dimer is less resolved as a result of orientation bias. The DNA flanking α2-helices provide fit confidence for the middle NanR dimer (green, inset). d Each NanR dimer is offset by approximately one half turn of the DNA helix. e Each GGTATA repeat of the DNA operator (in red) is separated by less than half a turn of the DNA helix. f Zoomed view of the NanR–DNA interface highlighting how each NanR bound to the (GGTATA)3-repeat operator maintains an analogous binding mode to the NanR-dimer1/DNA hetero-complex (Fig. 5), where the α3-helix binds in the major groove and the wing motif accommodates the minor groove of DNA. The N-terminal domains are hypothesized to interact with each other, given their proximity, through protein–protein interactions in the higher-order hetero-complex.
