The NF-kB p50 homodimer (mouse) is shown here complexed with a synthetic kB DNA motif. NF-kB is a transcription factor with DNA binding specificity for a 10 base-pair kB site present in the enhancers of many cellular target genes, including the immunoglobulin k light chain and major histocompatibility complex (MHC) class I gene enhancers. NF-kB is a member of the Rel family of transcription factors, all of which share sequence identity over a 300 amino acid "rel homology region", or RHR. (The RHR occupies most of the p50 protein structure shown here.)

Here is another view of the complex in which the secondary structure is color coded. Beta-sheets are shown in gold and alpha-helices are shown in pink. Rel family members form homo- and heterodimers which bind kB sites in the DNA. The RHR is responsible for both DNA binding and dimerization. It is the loops between the beta sheets of the RHR which make contact with the DNA. Each p50 unit contributes five loops which fill the entire major groove of the DNA. There is also an alpha helical segment which makes contact with the minor groove near the center of the kB element.

Here the p50 homodimer is shown without the DNA. Note the location of the loops between the beta sheets. Dimerization of the p50 units is mediated by hydrophobic interactions between hydrophobic amino acid residues in the beta sheets.

The loops contain a large number of positively charged residues localized within the protein-DNA interface, many of which are arginines and lysines. Two such lysines are depicted here. Lysine 241 is shown in yellow, and lysine 144 is shown in red. A closer look at the interactions of these residues with the DNA is shown here. Lysine 241 directly contacts the major groove, forming hydrogen bonds between the side chain nitrogen and oxygens in two of the bases in the DNA (bonds not shown). Lysine 144 interacts similarly with phosphate groups in the DNA backbone.

This is the same view with a CPK (Corey-Pauling-Kultin) color scheme.

references:

Ghosh G., van Duyne G., Ghosh S., Sigler P.B. Structure of NF-kB p50 homodimer bound to a kB site. (1995). Nature. 373, 303-310.

Muller C.W., Rey F.A., Sodeoka M., Verdine G.L., Harrison S.C. Structure of the NF-kB p50 homodimer bound to DNA. (1995). Nature. 373, 311-317.