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Yorodumi- PDB-3vd1: structure of p73 DNA binding domain tetramer modulates p73 transa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vd1 | ||||||
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Title | structure of p73 DNA binding domain tetramer modulates p73 transactivation | ||||||
Components |
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Keywords | ANTITUMOR PROTEIN/DNA / PROTEIN DNA COMPLEX / beta-immunoglobulin-like fold / TUMOUR SUPPRESSOR / ANTITUMOR 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 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 / regulation of mitotic cell cycle / kidney development / transcription corepressor binding / protein tetramerization / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / 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 / positive regulation of MAPK cascade / regulation of cell cycle / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / response to xenobiotic stimulus / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / 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: 2.95 Å | ||||||
Authors | Ethayathulla, A.S. / Tse, P.W. / Nguyen, S. / Viadiu, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structure of p73 DNA-binding domain tetramer modulates p73 transactivation. Authors: Ethayathulla, A.S. / Tse, P.W. / Monti, P. / Nguyen, S. / Inga, A. / Fronza, G. / Viadiu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vd1.cif.gz | 375.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vd1.ent.gz | 298.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vd1_validation.pdf.gz | 555.2 KB | Display | wwPDB validaton report |
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Full document | 3vd1_full_validation.pdf.gz | 658 KB | Display | |
Data in XML | 3vd1_validation.xml.gz | 73.1 KB | Display | |
Data in CIF | 3vd1_validation.cif.gz | 97.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/3vd1 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/3vd1 | HTTPS FTP |
-Related structure data
Related structure data | 3vd0C 3vd2C 3kmdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The octamer in the ASU corresponds to a tetramer p73DBD plus four chains of two continuous DNA double strands. |
-Components
#1: Protein | Mass: 23775.955 Da / Num. of mol.: 8 / Fragment: unp residue 115-312 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O15350 #2: DNA chain | Mass: 3664.380 Da / Num. of mol.: 8 / Source method: obtained synthetically #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 298 K / pH: 6.1 Details: 0.1M MES, 0.1M Na acetate, pH 6.1, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010 / Details: MIRROR |
Radiation | Monochromator: RH COATED FLAT MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→100 Å / Num. obs: 41946 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 35.6 Å2 / Rsym value: 0.06 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.4 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KMD Resolution: 2.95→19.99 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1510416.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.51 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.13 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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