8TKL

Murine NF-kappaB p50 Rel Homology Region homodimer in complex with a Test 16-mer kappaB-like DNA

Summary for 8TKL

• Entry DOI: 10.2210/pdb8tkl/pdb
• Descriptor: Nuclear factor NF-kappa-B p50 subunit, Test 17-mer kappaB-like DNA (3 entities in total)
• Functional Keywords: dna, nf-kappab, p50, transcription, transcription-dna complex, transcription/dna
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 4
• Total formula weight: 80265.50

Authors

Mitchel, S.,Mealka, M.,Rogers, W.E.,Milani, C.,Acuna, L.M.,Huxford, T. (deposition date: 2023-07-25, release date: 2023-10-18, Last modification date: 2024-10-09)

Primary citation

Zhu, N.,Mealka, M.,Mitchel, S.,Milani, C.,Acuna, L.M.,Rogers, E.,Lahana, A.N.,Huxford, T.
X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA.
Biomolecules, 13:-, 2023

PubMed Abstract: Though originally characterized as an inactive or transcriptionally repressive factor, the NF-κB p50 homodimer has become appreciated as a physiologically relevant driver of specific target gene expression. By virtue of its low affinity for cytoplasmic IκB protein inhibitors, p50 accumulates in the nucleus of resting cells, where it is a binding target for the transcriptional co-activator IκBζ. In this study, we employed X-ray crystallography to analyze the structure of the p50 homodimer on κB DNA from the promoters of human interleukin-6 (IL-6) and neutrophil-gelatinase-associated lipocalin (NGAL) genes, both of which respond to IκBζ. The NF-κB p50 homodimer binds 11-bp on IL-6 κB DNA, while, on NGAL κB DNA, the spacing is 12-bp. This begs the question: what DNA binding mode is preferred by NF-κB p50 homodimer? To address this, we engineered a "Test" κB-like DNA containing the core sequence 5'-GGGGAATTCCCC-3' and determined its X-ray crystal structure in complex with p50. This revealed that, when presented with multiple options, NF-κB p50 homodimer prefers to bind 11-bp, which necessarily imposes asymmetry on the complex despite the symmetry inherent in both the protein and its target DNA, and that the p50 dimerization domain can contact DNA via distinct modes.

PubMed: 37759710
DOI: 10.3390/biom13091310

Experimental method

X-RAY DIFFRACTION (3 Å)