Structure of NF-κB p50/p65 Heterodimer Bound to the PRDII DNA Element from the Interferon-β Promoter  Carlos R. Escalante, Leyi Shen, Dimitris Thanos, Aneel K. Aggarwal  Structure  Volume 10, Issue 3, Pages 383-391 (March 2002) DOI: 10.1016/S0969-2126(02)00723-2

Figure 1 DNA Sequences (A) Sequence alignment of κB elements found in the interferon-β promoter (PRDII), intronic enhancer of the immunoglobulin κ light chain gene (Ig-κB), MHC class I enhancer (MHC), and an idealized κB site (Ig). The conserved GG cores are enclosed in boxes. (B) Sequence of the DNA duplex, derived from the interferon-β promoter, used in cocrystallization. The core PRDII element is boxed. Structure 2002 10, 383-391DOI: (10.1016/S0969-2126(02)00723-2)

Figure 2 Overall View of the Structure (A) Ribbon diagram of the p65/p50 heterodimer bound to the PRDII element, viewed down the DNA helical axis. The p50 subunit is shown in blue and the p65 subunit in red. The DNA is shown in gold. The secondary elements, loops, and N and C termini are labeled. (B) Stereo representation of a Cα trace of the complex, with every twentieth residue labeled. Structure 2002 10, 383-391DOI: (10.1016/S0969-2126(02)00723-2)

Figure 3 Comparison of the NF-κB50/65-PRDII (Red) and NF-κB50/65-Ig (Blue) Complexes (A) p50 subunits viewed perpendicular to the DNA axis. The structures were superimposed based on the Cα atoms of the dimerization domains. (B) The two complexes viewed down the DNA helical axis (rmsd ∼2 Å). Structure 2002 10, 383-391DOI: (10.1016/S0969-2126(02)00723-2)

Figure 4 Protein-DNA Contacts Dashed arrows denote specific hydrogen bonds; solid lines represent phosphate contacts; striated lines denote van der Waals contacts. White circles correspond to the p50 subunit and gray circles to the p65 subunit. Nucleotides belonging to the GG core are shown in bold. Structure 2002 10, 383-391DOI: (10.1016/S0969-2126(02)00723-2)

Figure 5 Comparison of van der Waals Interactions between Tyr57 and the Inner DNA Bases (A) In the NF-κB50/65-PRDII structure, Tyr57 is shown interacting with the methyl groups of adjacent A:T base pairs. (B) In the NF-κB50/65-Ig structure, the thymine of the single A:T base pair rolls and twists out of plane. Structure 2002 10, 383-391DOI: (10.1016/S0969-2126(02)00723-2)

Figure 6 Comparison of the Relative Positioning of the PRDII (Red) and Ig-κB (Blue) DNAs The two complexes were aligned based on a superposition of the dimerization domain. Note that the PRDII phosphate backbone is almost 5 Å away from the p65 dimerization domain, while in the Ig-κB structure, the backbone is close enough for the p65 to make direct contacts with the phosphates. Structure 2002 10, 383-391DOI: (10.1016/S0969-2126(02)00723-2)

Figure 7 Comparison of DNA Curvature of the Central Ten Base Pairs The PRDII element has an overall curvature of 12°, while the Ig-κB site is double kinked with an overall curvature of 3°. DNA helical axes were calculated with the program CURVES [14]. Structure 2002 10, 383-391DOI: (10.1016/S0969-2126(02)00723-2)

Figure 8 Effect of DNA Allostery on IRF-1/NF-κB Assembly The IRF1-PRDI structure (green) is shown modeled next to NF-κB50/65-PRDII (red) and the NF-κB50/65-Ig (blue) complexes. IRF-1 (loop 2) sterically overlaps with the p50 subunit in the NF-κB50/65-Ig complex but not with the NF-κB50/65-PRDII complex. The relative movement of the p50 subunit in the NF-κB50/65-PRDII complex steers loop L6 clear of any steric clashes with loop L2 of the IRF-1 molecule. The distance between loops L6 in the two NF-κB complexes is as much as 11 Å. Structure 2002 10, 383-391DOI: (10.1016/S0969-2126(02)00723-2)