Computational protocol: Structure of p300 bound to MEF2 on DNA reveals a mechanism of enhanceosome assembly

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Protocol publication

[…] The crystals were transferred into the cryo-buffer of 32% PEG 1K and 50 mM BTP pH 6.3 and flash frozen in liquid nitrogen. The data were collected in Advanced Light Source (ALS 8.2.1, Berkeley). Data were processed by HKL2000 (). The p300:MEF2:DNA complex structure was solved by the molecular replacement method using the MEF2A:DNA crystal structure as a partial search model in Phaser (,). The initial search by molecular replacement located three MEF2:DNA complexes in the asymmetric unit. Electron density calculated using phases generated from the partial model revealed clearly the position of the p300 TAZ2 domain. Model building was carried out in O and Coot (,). The refinement was carried out using CNS (,) and the model was analyzed using programs from CCP4 (). The Ramachadran plot of the final model has 96.7% of residues in the favorite region and 3.3% of residues in the allowed region and no residue in the disallowed region. All figures were prepared in Pymol (The Pymol Molecular Graphics System, DeLano Scientific LLC). […]

Pipeline specifications

Software tools Coot, CNS, CCP4, PyMOL
Application Protein structure analysis
Organisms Homo sapiens