3KMD

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

Summary for 3KMD

• Entry DOI: 10.2210/pdb3kmd/pdb
• Descriptor: Cellular tumor antigen p53, 5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3', ZINC ION, ... (4 entities in total)
• Functional Keywords: p53 core domain, protein-dna interaction, self assembled tetramer, activator, apoptosis, cell cycle, disease mutation, dna-binding, endoplasmic reticulum, glycoprotein, host-virus interaction, isopeptide bond, li-fraumeni syndrome, metal-binding, methylation, nucleus, phosphoprotein, transcription, transcription regulation, tumor suppressor, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm. Isoform 1: Nucleus. Isoform 2: Nucleus. Isoform 3: Nucleus. Isoform 4: Nucleus. Isoform 7: Nucleus. Isoform 8: Nucleus. Isoform 9: Cytoplasm: P04637
• Total number of polymer chains: 6
• Total formula weight: 102073.67

Authors

Chen, Y.,Dey, R.,Chen, L. (deposition date: 2009-11-10, release date: 2010-02-23, Last modification date: 2023-09-06)

Primary citation

Chen, Y.,Dey, R.,Chen, L.
Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer.
Structure, 18:246-256, 2010

PubMed Abstract: 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.

PubMed: 20159469
DOI: 10.1016/j.str.2009.11.011

Experimental method

X-RAY DIFFRACTION (2.15 Å)