+Open data
-Basic information
Entry | Database: PDB / ID: 1veg | ||||||
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Title | Solution Structure of RSGI RUH-012, a UBA Domain from Mouse cDNA | ||||||
Components | NEDD8 ultimate buster-1 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ubiquitin associated domain / UBA domain / three helix bundle / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of ubiquitin-dependent protein catabolic process / Neddylation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleolus / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dyanamics | ||||||
Authors | Abe, T. / Hirota, H. / Izumi, K. / Yoshida, M. / Yamazaki, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of RSGI RUH-012, a UBA Domain from Mouse cDNA Authors: Abe, T. / Hirota, H. / Izumi, K. / Yoshida, M. / Yamazaki, 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 | 1veg.cif.gz | 456.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1veg.ent.gz | 381.1 KB | Display | PDB format |
PDBx/mmJSON format | 1veg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1veg ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1veg | 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: 8671.342 Da / Num. of mol.: 1 / Fragment: UBA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis system Gene: Mus musculus adult male medulla oblongata cDNA, RIKEN full-length enriched library, clone:6330412F12 product:NY-REN-18 antigen, full insert sequence Plasmid: P030324-39 / References: UniProt: P54729 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1.1mM RSGI RUH-012 U-15N, 13C; 20mM PiNa buffer; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100mM / pH: 6.0 / 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: JEOL ECA / Manufacturer: JEOL / Model: ECA / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dyanamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy and target function | ||||||||||||||||||||||||
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 |