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Yorodumi- PDB-3igl: Diversity in DNA recognition by p53 revealed by crystal structure... -
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-Basic information
Entry | Database: PDB / ID: 3igl | ||||||
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Title | Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 1) | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / P53 / MUTANT PROTEIN / LOOP-SHEET-HELIX MOTIF / DNA TARGET / ACTIVATOR / ANTI-ONCOGENE APOPTOSIS / CELL CYCLE / COVALENT PROTEIN-RNA LINKAGE / DISEASE MUTATION / DNA-BINDING / ENDOPLASMIC RETICULUM / GLYCOPROTEIN / HOST-VIRUS INTERACTION / LI-FRAUMENI SYNDROME / METAL-BINDING / METHYLATION / NUCLEUS / PHOSPHOPROTEIN / TRANSCRIPTION / TRANSCRIPTION REGULATION / TRANSCRIPTION/DNA COMPLE / Apoptosis / Isopeptide bond / Tumor suppressor / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...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 / 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 / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte 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 / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / response to salt stress Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kitayner, M. / Suad, O. / Rozenberg, H. / Shakked, Z. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs Authors: Kitayner, M. / Rozenberg, H. / Rohs, R. / Suad, O. / Rabinovich, D. / Honig, B. / Shakked, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3igl.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3igl.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 3igl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3igl_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 3igl_full_validation.pdf.gz | 449.8 KB | Display | |
Data in XML | 3igl_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 3igl_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/3igl ftp://data.pdbj.org/pub/pdb/validation_reports/ig/3igl | HTTPS FTP |
-Related structure data
Related structure data | 3igkSC 3kz8C S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 22505.582 Da / Num. of mol.: 1 / Fragment: P53 core domain, unp residues 94-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53 / Plasmid: PET27-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04637 |
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#2: DNA chain | Mass: 3664.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC DNA FRAGMENT. |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-EDO / |
#5: 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: 2.21 Å3/Da / Density % sol: 44.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.16M SODIUM ACETATE, 16% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 5, 2005 / Details: OSMIC INC. MSC-BLUE CONFOCAL MIRRORS |
Radiation | Monochromator: OSMIC INC. MSC - BLUE CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29 Å / Num. obs: 20255 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 27.68 Å2 / Rsym value: 0.049 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 974 / Rsym value: 0.225 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IGK Resolution: 1.8→24.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.438 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.753 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→24.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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