p53 tumour suppressor

Elena Orlova
Sinead Kearns
Andrei Okorokov
Ricardo Aramayo


Structure of p53 tumour suppressor by cryo-electron microscopy

A key factor in preventing us from developing cancer is the protein p53. The p53 tumour suppressor is a transcriptional activator that controls cell fate in response to various stresses. p53 can initiate cell cycle arrest, senescence and/or apoptosis via transactivation of p53 target genes, thus preventing cancer onset. Mutations that impair p53 usually occur in the core domain and negate the p53 sequence-specific DNA binding. Moreover, these mutations exhibit a dominant negative effect on the remaining wild-type p53.

The first structure of the complete p53 tetramer was determined using cryo-electron microscopy (Okorokov et al, 2006).The structure of mouse p53, stabilised with ATP, was found to resemble a hollow, skewed cube with symmetry D2. The cryo electron microscopy structure of the full-length p53 in complex with its specific DNA has been obtained at a resolution of 21 Ĺ. While two core domains from both dimers of the p53 tetramer interact with DNA within the complex, the other two core domains remain available for binding another DNA site. This finding helps to explain the dominant negative effect of p53 mutants based on the fact that p53 dimers are formed co-translationally before the whole tetramer assembles; therefore a single mutant dimer would prevent p53 tetramer from DNA binding.Comparison of the p53-DNA complex with our recent reconstruction of p53 tetramer 3D maps and fitting of the atomic model 2ata suggested that both of the p53 dimers interact with DNA and the dimers were oriented parallel to the DNA axis.The fit of the CT domains demonstrates that they are localized within the DNA contact regions providing additional interactions with DNA, thus enhancing the complex stability . On the other hand, the NT domains are located further away from DNA and do not participate in the p53-DNA complex formation but have room to interact with other proteins of the transcriptional machinery.The structure indicates that the Achilles’ heel of p53 is in its dimer-of-dimers organisation, thus the tetramer activity can be negated by mutation in only one allele followed by tumourigenesis. This model of p53 is compatible with the biochemical evidence and provides crucial insights into the mechanism of action of this protein, which is important as a cancer drug target(Aramayo et al, 2011).


3D reconstruction of p53-DNA complex. (A) Side and top views of the p53-DNA complex. The length of the stem is limited by the size of the image frames. (B) Superimposition of the DNA-free p53 map on the p53-DNA complex map. The two maps were compared in order to determine locations of core domains and dimers within the complex. N/C – areas of N and C termini interaction. (C) Stereo view of the crystal structure of two core domains bound to DNA (PDB entry: 2ata) fitted into the high density areas of the map (threshold used: 2s (light grey). (D) Fitting of the core domains and DNA in the EM map. Core domains are displayed in blue and red, DNA in orange. Docking was performed with both Chimera and Veda/UROX. The best fits from each software produced similar results.
R. Aramayo, M. B. Sherman, K. Brownless, A. L. Okorokov and E. V. Orlova. Quaternary structure of the specific p53-DNA complex reveals the mechanism of p53 mutant dominance. (2011) NAR, 39 (20), 8960-8971.

EM group web page Elena Orlova