Yi Mo, Benjamin Vaessen, Karen Johnston, Ronen Marmorstein

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Structures of SAP-1 Bound to DNA Targets from the E74 and c-fos Promoters Yi Mo, Benjamin Vaessen, Karen Johnston, Ronen Marmorstein Molecular Cell Volume 2, Issue 2, Pages 201-212 (August 1998) DOI: 10.1016/S1097-2765(00)80130-6

Figure 1 The SAP-1 ETS Domain, Its DNA Target Sites, and SAP-1/DNA Interactions (A) Amino acid sequences of the ETS domain of SAP-1 (used in the crystallographic studies), Elk-1, and other members of the family for which structural information is available. The secondary structural segments as assigned by PROMOTIF (Hutchinson and Thornton 1996) are labeled above the sequence. α helices are represented by wide rectangles, 310-helices by narrow rectangles, and β strands by bold arrows. Strictly conserved residues in the hydrophobic protein core are indicated with closed diamonds, and strictly conserved residue that make DNA contacts are indicated with open triangles. Highly conserved residues are colored in red, and residues that make nonconserved DNA contacts are colored in blue. (B) DNA target sites used in the crystallographic analyses. The GGA core sequence is indicated in green, and the sequence variations between the E74 and c-fos targets are indicated in red. The numbering schemes are shown above and below the sequences. (C) Schematic diagram of SAP-1/DNA interactions in the SAP-1/E74DNA and SAP-1/c-fosDNA complexes. Residues for the SAP-1 recognition helix are indicated with green boxes. Hydrogen bonds are indicated with black arrows, van der Waals contacts with blue arrows, and contacts that differ between the two complexes with red arrows. Water molecules that mediate protein–DNA contacts are represented by black balls. (D) 3.0 Å MIR electron density map of the SAP-1-E74DNA interface after solvent flattening. The map is contoured at 0.8 σ. Molecular Cell 1998 2, 201-212DOI: (10.1016/S1097-2765(00)80130-6)

Figure 2 Overall Structures of the SAP-1/E74DNA and SAP-1/c-fosDNA Complexes and Their Relationship to Other ETS Domain/DNA Structures (A) Ribbon diagram of the SAP-1/E74DNA complex viewed orthogonally to the DNA axis. The component segments are colored in blue (α helices), purple (310 helices), yellow (β strands), and red (DNA). The SAP-1/c-fosDNA structure is identical at the resolution shown. (B) SAP-1/E74DNA complex viewed orthogonally to (A), showing a pronounced hole down the DNA helical axis characteristic of A-form DNA. (C) Superposition of the Cα atoms of SAP-1 (blue), GABPα (green), and PU.1 (aqua) complexes using the central nine base pairs for the superposition. For clarity, only the E74DNA target (red) is shown. (D) Superposition of the DNA targets of the SAP-1/E74DNA (blue), GABPα/β/DNA(green), and PU.1/DNA (aqua) complexes using the protein Cα atoms for the superposition. Only the SAP-1 protein (red) is shown for clarity. (A), (B), (D), and (E) were created with the programs MOLSCRIPT (Kraulis 1991) and RASTER3D (Merritt and Murphy 1994). Molecular Cell 1998 2, 201-212DOI: (10.1016/S1097-2765(00)80130-6)

Figure 3 Protein–DNA Interactions Mediated by the α3 Recognition Helix of SAP-1, GABPα, and PU.1 (A) SAP-1/E74DNA complex. Only protein residues that make base-specific DNA contacts are shown. Hydrogen bonds are indicated by green dotted lines, van der Waals interactions are indicated with blue dotted lines, and water molecules are indicated by pink balls. The GGA core DNA sequence is shown in green, and nonconserved DNA bases flanking the GGA core sequence are shown in yellow. Figure 3 was created with the program SETOR (Evans 1993). (B) SAP-1/c-fosDNA complex. (C) GABPα/DNA complex. (D) PU.1/DNA complex. Molecular Cell 1998 2, 201-212DOI: (10.1016/S1097-2765(00)80130-6)

Figure 4 Model of the SAP-1 ETS Domain/SRF/SRE Ternary Complex (A) Overall view of the ternary complex. The model was prepared by combining the crystal coordinates of the SRF/DNA (Pellegrini et al. 1995) and SAP-1/c-fosDNA complexes. The SRF/DNA coordinates were transformed onto the SAP-1/DNA complex by superimposing the phosphate and C1′ atoms of the four overlapping base pairs in the two structures. The SAP-1/c-fosDNA complex is shown in blue and the SRF/DNA complex in red. The putative binding site for the B box in SAP-1 is connected to the C terminus of the SAP-1 ETS domain by a dotted line. (B) A close-up view of the recognition helices of the SAP-1 and SRF proteins in the DNA major groove. The side chains of the residues that are in position to mediate contacts between SAP-1 and SRF are highlighted in green. Molecular Cell 1998 2, 201-212DOI: (10.1016/S1097-2765(00)80130-6)