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Yorodumi- PDB-2cr8: Solution structure of the zf-RanBP domain of p53-binding protein Mdm4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cr8 | ||||||
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Title | Solution structure of the zf-RanBP domain of p53-binding protein Mdm4 | ||||||
Components | Mdm4 protein | ||||||
Keywords | CELL CYCLE / zf-RanBP domain / Mdm4 protein / p53-binding protein Mdm4 / Mdm2-like p53-binding DE protein / Mdmx protein / Double minute 4 protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process / Regulation of TP53 Activity through Methylation / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / cellular response to hypoxia / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / protein stabilization / Ub-specific processing proteases / regulation of cell cycle / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Zhang, H.P. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the zf-RanBP domain of p53-binding protein Mdm4 Authors: Zhang, H.P. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cr8.cif.gz | 312.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cr8.ent.gz | 259.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cr8_validation.pdf.gz | 340.1 KB | Display | wwPDB validaton report |
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Full document | 2cr8_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 2cr8_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2cr8_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/2cr8 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/2cr8 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 5967.539 Da / Num. of mol.: 1 / Fragment: zf-RanBP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: MDM4 / Plasmid: P040809-07 / References: UniProt: O15151 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.42mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZnCl2 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |