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Yorodumi- PDB-2wtt: Structure of the human p73 tetramerization domain (crystal form II) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wtt | ||||||
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Title | Structure of the human p73 tetramerization domain (crystal form II) | ||||||
Components | TUMOR PROTEIN P73 | ||||||
Keywords | TRANSCRIPTION / ALTERNATIVE SPLICING / OLIGOMERIZATION DOMAIN / CELL-CYCLE CONTROL / TRANSCRIPTION FACTOR / COOPERATIVITY / PHOSPHOPROTEIN / UBL CONJUGATION / ACTIVATOR / TUMOR SUPPRESSION / DEVELOPMENT / APOPTOSIS / CELL CYCLE / DNA BINDING / TRANSCRIPTION REGULATION | ||||||
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 / 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 / response to organonitrogen compound / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Joerger, A.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wtt.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wtt.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wtt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wtt_validation.pdf.gz | 530 KB | Display | wwPDB validaton report |
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Full document | 2wtt_full_validation.pdf.gz | 541.5 KB | Display | |
Data in XML | 2wtt_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 2wtt_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/2wtt ftp://data.pdbj.org/pub/pdb/validation_reports/wt/2wtt | HTTPS FTP |
-Related structure data
Related structure data | 2wqiSC 2wqjC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 6225.732 Da / Num. of mol.: 16 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 351-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O15350 #2: Water | ChemComp-HOH / | Sequence details | TWO ADDITIONAL | |
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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 Å3/Da / Density % sol: 39.8 % / Description: NONE |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: SITTING DROP VAPOR DIFFUSION AT 17 DEGREE C. PROTEIN SOLUTION: 15 MG/ML IN 20 MM TRIS (PH 8.5), 50 MM NACL. CRYSTALLIZATION BUFFER: 0.1 M SODIUM CITRATE (PH 6.2), 40% PEG 600. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→59.7 Å / Num. obs: 36567 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 11.6 % / Biso Wilson estimate: 34.87 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 5.9 / % possible all: 100 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WQI Resolution: 2.3→24.786 Å / SU ML: 0.39 / σ(F): 1.19 / Phase error: 28.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.313 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→24.786 Å
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Refine LS restraints |
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LS refinement shell |
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