Figure 2
From: New protein-DNA complexes in archaea: a small monomeric protein induces a sharp V-turn DNA structure
MC1 slightly adapts its conformation upon binding to the DNA15bp. (a) 3D solution structures of MC1 in its free (left) and bound (right) forms in cartoon representation. The β-strands and the α-helix are colorized in blue and red, respectively. (b) Primary and secondary structures of MC1 free (top) and bound (bottom): Blue arrows and red cylinder are for β - and α -structures, respectively, and black wickets for bulges. (c) Overlay of the cartoon representations of the free (dark grey) and bound (light grey) conformations of the MC1 protein. In order to highlight the conformational changes of MC1 upon binding, three couples of axes are represented: rotation of the α-helix by 10° around Ala32 in green, of the β1-strand by 10° around Val7 in magenta and of the β2-strand by 30° around Val18 in cyan. Close-up pictures of the side chains of Gln23, Arg25 and Gln26, in yellow (free MC1) and orange (bound MC1), show that their orientation have changed upon binding in order to be optimally positioned for an interaction with DNA. Alignment of the two MC1 structures, in their free and bound forms, give a rmsd of 4 Å (all residues) and a rmsd of 2.3 Å (without the arm).
