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Yorodumi- PDB-1v87: Solution Structure of the Ring-H2 Finger Domain of Mouse Deltex P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v87 | ||||||
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Title | Solution Structure of the Ring-H2 Finger Domain of Mouse Deltex Protein 2 | ||||||
Components | Deltex protein 2 | ||||||
Keywords | METAL BINDING PROTEIN / Ring-H2 Domain / Zinc-Binding Domain / Notch signaling / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Activated NOTCH1 Transmits Signal to the Nucleus / Notch signaling pathway / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / nuclear membrane / protein ubiquitination / zinc ion binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Miyamoto, K. / Muto, Y. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of the Ring-H2 Finger Domain of Mouse Deltex Protein 2 Authors: Miyamoto, K. / Muto, Y. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v87.cif.gz | 656.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v87.ent.gz | 545 KB | Display | PDB format |
PDBx/mmJSON format | 1v87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/1v87 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/1v87 | HTTPS FTP |
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-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: 12230.006 Da / Num. of mol.: 1 / Fragment: Ring-H2 Finger Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 2610524D08 / Plasmid: P030421-37 / References: UniProt: Q8R3P2 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.05mM Ring-H2 Domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.1mM ZnCl; 90% H2O, 10%D2O 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
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-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: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |