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Yorodumi- PDB-2l14: Structure of CBP nuclear coactivator binding domain in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 2l14 | ||||||
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Title | Structure of CBP nuclear coactivator binding domain in complex with p53 TAD | ||||||
Components |
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Keywords | PROTEIN BINDING / p53 / CBP / p300 / TAD | ||||||
Function / homology | Function and homology information Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex ...Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / Regulation of lipid metabolism by PPARalpha / negative regulation of viral process / Cytoprotection by HMOX1 / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / outer kinetochore / negative regulation of interferon-beta production / histone H3K27 acetyltransferase activity / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / MRF binding / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / : / : / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / peroxisome proliferator activated receptor binding / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / face morphogenesis / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / negative regulation of transcription by RNA polymerase I / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / positive regulation of dendritic spine development / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / peptide-lysine-N-acetyltransferase activity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / cellular response to hepatocyte growth factor stimulus / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / negative regulation of telomerase activity / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / non-canonical NF-kappaB signal transduction / behavioral response to cocaine / Zygotic genome activation (ZGA) / acetyltransferase activity / necroptotic process / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
Authors | Lee, C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structure of the p53 transactivation domain in complex with the nuclear receptor coactivator binding domain of CREB binding protein. Authors: Lee, C.W. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l14.cif.gz | 652.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l14.ent.gz | 569.8 KB | Display | PDB format |
PDBx/mmJSON format | 2l14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/2l14 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/2l14 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6568.562 Da / Num. of mol.: 1 / Fragment: CBP nuclear coactivator binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P45481 |
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#2: Protein/peptide | Mass: 5574.096 Da / Num. of mol.: 1 / Fragment: p53 TAD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-99% 15N] CBP nuclear coactivator binding domain, 0.5 mM [U-99% 15N] p53 TAD, 0.5 mM [U-99% 13C; U-99% 15N] CBP nuclear coactivator binding domain, 0.5 mM [U-99% 13C; U-99% 15N] ...Contents: 0.5 mM [U-99% 15N] CBP nuclear coactivator binding domain, 0.5 mM [U-99% 15N] p53 TAD, 0.5 mM [U-99% 13C; U-99% 15N] CBP nuclear coactivator binding domain, 0.5 mM [U-99% 13C; U-99% 15N] p53 TAD, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: AMBER / Version: 9 Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm Classification: refinement |
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Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |