Volume 10, Issue 10, Pages (October 2002)

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Volume 10, Issue 10, Pages 1395-1407 (October 2002) DNA Recognition by the RUNX1 Transcription Factor Is Mediated by an Allosteric Transition in the RUNT Domain and by DNA Bending Deborah Bartfeld, Linda Shimon, Graeme C. Couture, Dov Rabinovich, Felix Frolow, Ditsa Levanon, Yoram Groner, Zippora Shakked Structure Volume 10, Issue 10, Pages 1395-1407 (October 2002) DOI: 10.1016/S0969-2126(02)00853-5

Figure 1 Structures of the Free and Complexed Runt Domains (A) The two independent RD molecules of the present study superimposed on each other (shown in magenta and gold). The numbering scheme of the loops and β strands is as in [29]. All figures were produced with the MOLSCRIPT [58] and Raster3D [59] programs. (B) Amino acid sequence and the secondary structure of the free RD. (C) Comparison of the Runt domains from four crystal structures using Cα atoms: the free RD molecules from the present study (magenta and gold), from the RD/CBFβ complex (blue; ID code 1E50), from the RD/DNA complex (green; ID code 1HJC), and from the RD/CBFβ/DNA complex (cyan; ID code 1H9D). Structure 2002 10, 1395-1407DOI: (10.1016/S0969-2126(02)00853-5)

Figure 2 Comparison of the Loop Conformations in the Four RD Structures with the Same Color Scheme as in Figure 1 (A) A view of the three loops, L5, L9, and L11, and adjacent regions showing amino acids that interact with CBFβ and DNA. The corresponding side chain atoms that interact with CBFβ or DNA are highlighted for the ternary complex RD (cyan); atoms that interact with CBFβ are shown as red spheres (oxygen atoms), and those that interact with DNA are shown as blue spheres (nitrogen atoms). (B) Changes in the hydrophobic environment of the L11 loop as a consequence of binding to DNA or CBFβ. Structure 2002 10, 1395-1407DOI: (10.1016/S0969-2126(02)00853-5)

Figure 3 Conformational Changes in the Runt Domain upon Binding to DNA and to CBFβ (A) A view of the RD regions that interact with DNA. Superimposed are the corresponding structures of the free RD (magenta) and the RD/DNA complex (green). The amino acids that interact with the DNA are shown as transparent. The amino acids that stabilize this surface by intramolecular hydrogen bonds and van der Waals interactions are shown as solid. Attractive electrostatic interactions are shown as dotted lines. (B) A comparison between the two conformations of the L11 loop (L11-I and L11-II) and the associated orientations of the L9 loops in the free RD (magenta) and the DNA-bound RD (green). Side chains are transparent. Hydrogen bonds are shown as dotted lines. (C) A view showing the interactions of RD with CBFβ that stabilize the L11-II conformation. The hydrogen-bonded triad T161-D66-H163 of RD (cyan) is supported through hydrogen bonds and hydrophobic interactions with CBFβ (blue). The same region of RD from the RD/DNA complex (green) is also shown, for comparison. Structure 2002 10, 1395-1407DOI: (10.1016/S0969-2126(02)00853-5)

Figure 4 Comparison between the Free and the Complexed RD and DNA Molecules The free RD and its DNA target (magenta) superimposed on the corresponding molecules of the RD/CBFβ/DNA complex (cyan and blue). Structure 2002 10, 1395-1407DOI: (10.1016/S0969-2126(02)00853-5)

Figure 5 Stabilizing Interactions between Adjacent Loops in the Free and Complexed RD Structures (A) L5-L9 interactions in the free RD molecule (magenta) and in the RD/CBFβ/DNA complex (cyan). (B) Comparison of the top loops (L1, L4, L7, and L10) in the free and complexed RD structures. ID and color codes are as in Figure 1C. Amino acid side chains that are involved in intra- and interloop interactions are shown. For clarity, only interloop hydrogen bonds are shown (dotted lines). Atoms that interact with CBFβ in the RD/CBFβ/DNA complex (cyan) are shown as large spheres. Structure 2002 10, 1395-1407DOI: (10.1016/S0969-2126(02)00853-5)

Figure 6 Superposition of the Three DNA Binding Sites, Ten Base Pairs The free DNA (magenta), the DNA bound to RD (green; ID code 1HJC), and the DNA bound to RD/CBFβ (cyan; ID code 1H9D). The view is along the dyad axis through the center. Structure 2002 10, 1395-1407DOI: (10.1016/S0969-2126(02)00853-5)