+Open data
-Basic information
Entry | Database: PDB / ID: 4a63 | ||||||
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Title | Crystal structure of the p73-ASPP2 complex at 2.6A resolution | ||||||
Components |
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Keywords | CELL CYCLE / TP53BP2 / TUMOUR SUPPRESSOR / ANKYRINS / APOPTOSIS REGULATORY PROTEINS | ||||||
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 execution phase of apoptosis / 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 ...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 execution phase of apoptosis / 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 / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cell cycle / negative regulation of neuron differentiation / mismatch repair / NF-kappaB binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / MDM2/MDM4 family protein binding / response to organonitrogen compound / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / SH3 domain binding / 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 / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / cell cycle / positive regulation of apoptotic process / 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 / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Canning, P. / Sharpe, T. / Krojer, T. / Savitsky, P. / Cooper, C.D.O. / Salah, E. / Keates, T. / Muniz, J. / Vollmar, M. / von Delft, F. ...Canning, P. / Sharpe, T. / Krojer, T. / Savitsky, P. / Cooper, C.D.O. / Salah, E. / Keates, T. / Muniz, J. / Vollmar, M. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Bountra, C. / Edwards, A. / Bullock, A.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structural Basis for Aspp2 Recognition by the Tumor Suppressor P73. Authors: Canning, P. / von Delft, F. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a63.cif.gz | 479.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a63.ent.gz | 390 KB | Display | PDB format |
PDBx/mmJSON format | 4a63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/4a63 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a63 | HTTPS FTP |
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-Related structure data
Related structure data | 2xwcSC 1ycsS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23342.561 Da / Num. of mol.: 6 / Fragment: DNA-BINDING DOMAIN, RESIDUES 1-208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE2 / References: UniProt: O15350 #2: Protein | Mass: 26951.475 Da / Num. of mol.: 6 / Fragment: ANKYRIN AND SH3 DOMAINS, RESIDUES 892-1128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q13625 #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | Nonpolymer details | ACETATE (ACT): PRESENT IN CRYSTALLIZ | |
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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: 3.32 Å3/Da / Density % sol: 63.03 % / Description: NONE |
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Crystal grow | Details: 1.00M NA/KPO4, 0.1M ACETATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→88.72 Å / Num. obs: 111026 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 43.51 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2XWC AND 1YCS CHAIN B Resolution: 2.27→85.05 Å / Cor.coef. Fo:Fc: 0.7815 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.184 Details: INITIAL REFINEMENT WITH REFMAC BUSTER 2.1 PHENIX.XTRIAGE. THE ANALYSES OF THE PATTERSON FUNCTION REVEALS A SIGNIFICANT OFF-ORIGIN PEAK THAT IS 47.52 PERCENT OF THE ORIGIN PEAK, INDICATING ...Details: INITIAL REFINEMENT WITH REFMAC BUSTER 2.1 PHENIX.XTRIAGE. THE ANALYSES OF THE PATTERSON FUNCTION REVEALS A SIGNIFICANT OFF-ORIGIN PEAK THAT IS 47.52 PERCENT OF THE ORIGIN PEAK, INDICATING PSEUDO TRANSLATIONAL SYMMETRY. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=19288. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0 NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
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Displacement parameters | Biso mean: 51.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.305 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→85.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.33 Å / Total num. of bins used: 20
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