+Open data
-Basic information
Entry | Database: PDB / ID: 1vdl | ||||||
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Title | Solution Structure of RSGI RUH-013, a UBA domain in Mouse cDNA | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 25 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / UBA domain / Mouse cDNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of ERAD pathway / SUMO binding / protein K48-linked deubiquitination / Ub-specific processing proteases / protein K63-linked deubiquitination / protein deubiquitination / proteasome complex / ATPase binding / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 ...negative regulation of ERAD pathway / SUMO binding / protein K48-linked deubiquitination / Ub-specific processing proteases / protein K63-linked deubiquitination / protein deubiquitination / proteasome complex / ATPase binding / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / endoplasmic reticulum / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Doi-Katayama, Y. / Hirota, H. / Saito, K. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of RSGI RUH-013, a UBA domain in Mouse cDNA Authors: Doi-Katayama, Y. / Hirota, H. / Saito, K. / Koshiba, S. / 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 | 1vdl.cif.gz | 453.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vdl.ent.gz | 380.4 KB | Display | PDB format |
PDBx/mmJSON format | 1vdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/1vdl ftp://data.pdbj.org/pub/pdb/validation_reports/vd/1vdl | 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: 8417.175 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 (E.coli) / Gene: RIKEN cDNA 2610101O11 / Plasmid: P030324-44 / References: UniProt: P57080, EC: 3.1.2.15 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.3mM UBA domain U-15N, 13C; 20mM phosphate buffer (pH 6.0); 100mM NaCl; 1mM DTT/0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM NaCl / 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: 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 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 |