An atomic model of the interferon-beta enhanceosome

Abstract

Transcriptional activation of the interferon-beta (IFN-beta) gene requires assembly of an enhanceosome containing ATF-2/c-Jun, IRF-3/IRF-7, and NFkappaB. These factors bind cooperatively to the IFN-beta enhancer and recruit coactivators and chromatin-remodeling proteins to the IFN-beta promoter. We describe here a crystal structure of the DNA-binding domains of IRF-3, IRF-7, and NFkappaB, bound to one half of the enhancer, and use a previously described structure of the remaining half to assemble a complete picture of enhanceosome architecture in the vicinity of the DNA. Association of eight proteins with the enhancer creates a continuous surface for recognizing a composite DNA-binding element. Paucity of local protein-protein contacts suggests that cooperative occupancy of the enhancer comes from both binding-induced changes in DNA conformation and interactions with additional components such as CBP. Contacts with virtually every nucleotide pair account for the evolutionary invariance of the enhancer sequence.

Figure 1

Strategy for assembling the complete INF-β enhanceosome structure. Three sets of overlapping crystal structures were determined. (A) ATF-2/c-Jun in complex with two IRF-3 molecules on the PRDIV and PRDIII regions of the enhancer (Panne et al., 2004). (B) NFκB in complex with IRF-7 and IRF-3 on PRDI-PRDII. (C) Four IRF-3 molecules in complex with the full length enhancer. (D) Fully assembled INF-β enhanceosome.

Figure 2

Structure of the NFκB:IRF-7:IRF-3:DNA complex. Ribbons representation of the complex viewed (A) normal to and (B) along the DNA helical axis. The Rel-homology region (RHR) of p50 is in light blue; that of RelA, in dark blue. IRF-7D is in yellow; IRF-3C, in green. The two DNA strands are in grey. (C) Sequence of the DNA duplex corresponding to the PRDI-II region of the IFN-β enhancer (−85 to −51 nucleotides from the start site of transcription). (D) Protein-DNA contacts of IRF-3C. (E) Protein-DNA contacts of IRF-7D.

Figure 3

Protein-DNA contacts. Schematic diagram of protein-DNA contacts generated using NUCPLOT (Luscombe et al., 1997). Residues from ATF-2 are in red, c-Jun, in dark red, IRF-3A and C, in green, and IRF-7B and D, in yellow. The RHR of p50 is in light blue; that of RelA, in dark blue. The core binding sites for each protein are indicated in the corresponding colors. Blue lines indicate hydrogen bonds; red lines, van der Waals contacts.

Figure 4

Overall structure of the interferon-β enhanceosome: (A) Side view of the complex, showing bending of the DNA around the four IRF domains. The red line shows the local DNA helical axis as calculated with the program Curves (Lavery and Sklenar, 1988). The RHR of p50 is in light blue; that of RelA, in dark blue. IRF-7B and D are in yellow; IRF-3A and C, in green. ATF-2 is in light red; c-Jun, in dark red. The two DNA strands are in grey. (B) Molecular surface representation of the interferon-β enhanceosome showing that the eight polypetides form a composite surface for DNA recognition. The two views, related by a 180° rotation as suggested by the arrow, are from opposite sides of the complex.