+Open data
-Basic information
Entry | Database: PDB / ID: 2ioi | ||||||
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Title | Crystal structure of the mouse p53 core domain at 1.55 A | ||||||
Components | Cellular tumor antigen p53P53 | ||||||
Keywords | TRANSCRIPTION / ANTITUMOR PROTEIN / IG fold | ||||||
Function / homology | Function and homology information Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Transcriptional activation of cell cycle inhibitor p21 / Regulation of TP53 Activity through Association with Co-factors / RUNX3 regulates CDKN1A transcription / regulation of thymocyte apoptotic process / PI5P Regulates TP53 Acetylation / DNA Damage/Telomere Stress Induced Senescence / Stabilization of p53 ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Transcriptional activation of cell cycle inhibitor p21 / Regulation of TP53 Activity through Association with Co-factors / RUNX3 regulates CDKN1A transcription / regulation of thymocyte apoptotic process / PI5P Regulates TP53 Acetylation / DNA Damage/Telomere Stress Induced Senescence / Stabilization of p53 / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / Regulation of TP53 Degradation / Oncogene Induced Senescence / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Ovarian tumor domain proteases / PKR-mediated signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of cellular senescence / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Ub-specific processing proteases / negative regulation of DNA biosynthetic process / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing 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 / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / embryo development ending in birth or egg hatching / histone deacetylase regulator activity / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of leukocyte migration / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / positive regulation of execution phase of apoptosis / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / T cell proliferation involved in immune response / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / necroptotic process / rRNA transcription / positive regulation of release of cytochrome c from mitochondria / TFIID-class transcription factor complex binding / mitophagy / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of mitotic cell cycle / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / chromosome organization / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to glucose starvation / cellular response to actinomycin D / somitogenesis / positive regulation of cell cycle / type II interferon-mediated signaling pathway / regulation of neuron apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / gastrulation / response to UV / negative regulation of fibroblast proliferation Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Ho, W.C. / Luo, C. / Zhao, K. / Chai, X. / Fitzgerald, M.X. / Marmorstein, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds. Authors: Ho, W.C. / Luo, C. / Zhao, K. / Chai, X. / Fitzgerald, M.X. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ioi.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ioi.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ioi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/2ioi ftp://data.pdbj.org/pub/pdb/validation_reports/io/2ioi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22814.057 Da / Num. of mol.: 1 / Fragment: Core domain, residues 92-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tp53, P53, Trp53 / Plasmid: pRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02340 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-TRS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Tris, 16-18% PEG 2K MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 30053 / Rmerge(I) obs: 0.04 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.55→30 Å / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 11.7 / Num. unique all: 30053 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→30 Å / Isotropic thermal model: Anisotropic / Cross valid method: Rfree / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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