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Yorodumi- PDB-4g83: Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a F... -
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-Basic information
Entry | Database: PDB / ID: 4g83 | ||||||
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Title | Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / BETA-IMMUNOGLOBULIN FOLD / TUMOR SUPPRESSOR / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / 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 / regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / 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 / regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / mismatch repair / MDM2/MDM4 family protein binding / : / transcription corepressor binding / kidney development / protein tetramerization / p53 binding / intrinsic apoptotic signaling pathway in response to DNA damage / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / positive regulation of MAPK cascade / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / protein kinase binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Ethayathulla, A.S. / Viadiu, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element Authors: Ethayathulla, A.S. / Viadiu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g83.cif.gz | 199.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g83.ent.gz | 156.4 KB | Display | PDB format |
PDBx/mmJSON format | 4g83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g83_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 4g83_full_validation.pdf.gz | 475.5 KB | Display | |
Data in XML | 4g83_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 4g83_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/4g83 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/4g83 | HTTPS FTP |
-Related structure data
Related structure data | 4g82C 3vd0S 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: DNA chain | Mass: 6134.966 Da / Num. of mol.: 2 / Fragment: unp residues 115-312 / Source method: obtained synthetically / Details: dna synthesized #2: Protein | Mass: 23775.955 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN, P73, TP73 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15350 #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M BTP, 20% PEG3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2012 / Details: mirror |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. all: 8957 / Num. obs: 5072 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3vd0 Resolution: 4→45.61 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.887 / SU ML: 0.39 / Isotropic thermal model: TLS refinement / σ(F): 1.35 / Phase error: 28.13 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.022 Å2
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Refinement step | Cycle: LAST / Resolution: 4→45.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.0002→45.6125 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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