Different steps of the 3D model construction of DNA-(Slr1738)2 complex. A - Superposition of [protein-DNA] X-ray structure with (Slr1738)2 based on recognition helix H4 of monomer A. B - Structure of (Slr1738)2 docked to X-ray DNA (monomer A is well-positioned). C - DNA sequence modification. D - Structure of the Slr1738 monomer A (orange) well docked to the DNA molecule and ideal positioning of the monomer B (yellow). E - Matching on DNA sequence of both structures in D which give rise to a bad dimerization interface for Slr1738. F - (Slr1738)2 with a well defined dimerization interface, in green, matched on the protein structure E, in light orange. G - Minimization protocol consisting in application of harmonic distance restraints on both the DNA recognition helices. H - Final structure.
Garcin et al. BMC Structural Biology 2012 12:1 doi:10.1186/1472-6807-12-1