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- PDB-2wqj: Crystal structure of a truncated variant of the human p73 tetrame... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wqj | ||||||
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Title | Crystal structure of a truncated variant of the human p73 tetramerization domain | ||||||
![]() | TUMOR PROTEIN P73 | ||||||
![]() | TRANSCRIPTION / P73 / P63 / P53 / TUMOR SUPPRESSION / TRANSCRIPTION FACTOR / TETRAMER / HEXAMER / OLIGOMERIZATION DOMAIN / DNA-BINDING / COOPERATIVITY / CELL-CYCLE CONTROL / TRANSCRIPTION REGULATION / APOPTOSIS / CELL CYCLE / DEVELOPMENT | ||||||
Function / homology | ![]() 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation ...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 / 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 / transcription corepressor binding / kidney development / 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 / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joerger, A.C. | ||||||
![]() | ![]() Title: Structural Evolution of P53, P63, and P73: Implication for Heterotetramer Formation. Authors: Joerger, A.C. / Rajagopalan, S. / Natan, E. / Veprintsev, D.B. / Robinson, C.V. / Fersht, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.9 KB | Display | ![]() |
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PDB format | ![]() | 147.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 564.7 KB | Display | ![]() |
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Full document | ![]() | 570 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 48.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 4178.738 Da / Num. of mol.: 28 Fragment: TRUNCATED TETRAMERIZATION DOMAIN, RESIDUES 351-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | TWO ADDITIONAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: SITTING DROP VAPOR DIFFUSION AT 17 DEGREE C. PROTEIN SOLUTION: 10 MG/ML IN 20 MM TRIS (PH 8.5), 50 MM NACL. CRYSTALLIZATION BUFFER: 0.1 M TRIS (PH 8.5), 0.9 M AMMONIUM PHOSPHATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2→76.4 Å / Num. obs: 90937 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 34.31 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3 |
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Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2→24.96 Å / SU ML: 0.29 / σ(F): 1.08 / Phase error: 25.49 / Stereochemistry target values: ML Details: THIS ENTRY REPORTS THE STRUCTURE OF A TRUNCATED FORM OF THE P73 TETRAMERIZATION DOMAIN (RESIDUES 351-383)THAT LACKS A C-TERMINAL HELIX THAT IS ESSENTIAL FOR STABILIZING THE OVERALL ...Details: THIS ENTRY REPORTS THE STRUCTURE OF A TRUNCATED FORM OF THE P73 TETRAMERIZATION DOMAIN (RESIDUES 351-383)THAT LACKS A C-TERMINAL HELIX THAT IS ESSENTIAL FOR STABILIZING THE OVERALL ARCHITECTURE OF THE P73 TETRAMER. SEE PDB ENTRY 2WQI WITH THE STRUCTURE OF P73 RESIDUES 351-399 FOR COMPARISON.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.14 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2→24.96 Å
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Refine LS restraints |
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LS refinement shell |
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