3KMD: Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer

Recent studies suggest that p53 binds predominantly to consensus sites composed of two decameric half-sites with zero spacing in vivo. Here we report the crystal structure of the p53 core domain bound to a full consensus site as a tetramer at 2.13A resolution. Comparison with previously reported structures of p53 dimer:DNA complexes and a chemically trapped p53 tetramer:DNA complex reveals that DNA binding by the p53 core domain is a cooperative self-assembling process accompanied by structural changes of the p53 dimer and DNA. Each p53 monomer interacts with its two neighboring subunits through two different protein-protein interfaces. The DNA is largely B-form and shows no discernible bend, but the central base-pairs between the two half-sites display a significant slide. The extensive protein-protein and protein-DNA interactions explain the high cooperativity and kinetic stability of p53 binding to contiguous decameric sites and the conservation of such binding-site configuration in vivo.
PDB ID: 3KMDDownload
MMDB ID: 80277
PDB Deposition Date: 2009/11/10
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.15  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 3KMD: hexameric; determined by author
Molecular Components in 3KMD
Label Count Molecule
Proteins (4 molecules)
Cellular Tumor Antigen P53(Gene symbol: TP53)
Molecule annotation
Nucleotide(1 molecule)
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB