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Yorodumi- PDB-1ujd: Solution Structure of RSGI RUH-003, a PDZ domain of hypothetical ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ujd | ||||||
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Title | Solution Structure of RSGI RUH-003, a PDZ domain of hypothetical KIAA0559 protein from human cDNA | ||||||
Components | KIAA0559 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ domain / human cdna / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information presynaptic active zone assembly / presynapse to nucleus signaling pathway / structural constituent of presynaptic active zone / cytoskeleton of presynaptic active zone / profilin binding / protein localization to synapse / regulation of exocytosis / calcium-dependent phospholipid binding / insulin secretion / synaptic vesicle exocytosis ...presynaptic active zone assembly / presynapse to nucleus signaling pathway / structural constituent of presynaptic active zone / cytoskeleton of presynaptic active zone / profilin binding / protein localization to synapse / regulation of exocytosis / calcium-dependent phospholipid binding / insulin secretion / synaptic vesicle exocytosis / GABA-ergic synapse / cytoskeleton organization / cAMP-mediated signaling / postsynaptic density / cytoskeleton / axon / glutamatergic synapse / synapse / calcium ion binding / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Ohashi, W. / Hirota, H. / Yamazaki, T. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution Structure of RSGI RUH-003, a PDZ domain of hypothetical KIAA0559 protein from human cDNA Authors: Ohashi, W. / Hirota, H. / Yamazaki, T. / Muto, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ujd.cif.gz | 666.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ujd.ent.gz | 556.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ujd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ujd_validation.pdf.gz | 343 KB | Display | wwPDB validaton report |
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Full document | 1ujd_full_validation.pdf.gz | 508.5 KB | Display | |
Data in XML | 1ujd_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 1ujd_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/1ujd ftp://data.pdbj.org/pub/pdb/validation_reports/uj/1ujd | 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: 12279.770 Da / Num. of mol.: 1 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / References: UniProt: Q9Y6V0 |
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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: 1.5mM RSGI RUH-003 U-13C,15N; 20mM Tris-HCl, 100mM NaCl, 1mM DTT U-2H, 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100mM NaCl / 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: simulated annealing, torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest target function | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: The submitted conformer models are those with the lowest number of target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |