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Yorodumi- PDB-1uit: Solution structure of RSGI RUH-006, The third PDZ domain OF hDlg5... -
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-Basic information
Entry | Database: PDB / ID: 1uit | ||||||
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Title | Solution structure of RSGI RUH-006, The third PDZ domain OF hDlg5 (KIAA0583) protein [Homo sapiens] | ||||||
Components | HUMAN DISCS LARGE 5 PROTEIN | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ domain / hDlg5 / MAGUK family / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information zonula adherens assembly / positive regulation of hippo signaling / polarized epithelial cell differentiation / protein localization to adherens junction / maintenance of cell polarity / apical protein localization / metanephric collecting duct development / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of smoothened signaling pathway / positive regulation of synapse assembly ...zonula adherens assembly / positive regulation of hippo signaling / polarized epithelial cell differentiation / protein localization to adherens junction / maintenance of cell polarity / apical protein localization / metanephric collecting duct development / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of smoothened signaling pathway / positive regulation of synapse assembly / midbrain development / epithelial tube branching involved in lung morphogenesis / positive regulation of dendritic spine development / negative regulation of hippo signaling / epithelial to mesenchymal transition / negative regulation of T cell proliferation / cytoskeletal protein binding / ciliary basal body / negative regulation of cell migration / adherens junction / cell-cell adhesion / beta-catenin binding / cell junction / signaling receptor complex adaptor activity / protein-containing complex assembly / regulation of apoptotic process / postsynaptic density / intracellular signal transduction / negative regulation of cell population proliferation / signal transduction / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Abe, T. / Hirota, H. / Kobayashi, N. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of RSGI RUH-006, The third PDZ domain OF hDlg5 (KIAA0583) protein [Homo sapiens] Authors: Abe, T. / Hirota, H. / Kobayashi, N. / 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 | 1uit.cif.gz | 679.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uit.ent.gz | 569.7 KB | Display | PDB format |
PDBx/mmJSON format | 1uit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uit_validation.pdf.gz | 343 KB | Display | wwPDB validaton report |
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Full document | 1uit_full_validation.pdf.gz | 517.4 KB | Display | |
Data in XML | 1uit_validation.xml.gz | 44.7 KB | Display | |
Data in CIF | 1uit_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/1uit ftp://data.pdbj.org/pub/pdb/validation_reports/ui/1uit | 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: 12499.833 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 system / Gene: Kazusa cDNA hj00729 / Plasmid: P021030-24 / References: UniProt: Q8TDM6 |
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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: 1.3mM RSGI RUH-006 U-15N, 13C; 20mM d-Tris-HCl buffer; 100mM NaCl; 1mM d-DTT; 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 / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / 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: the structure with the lowest energy and score of target function was selected. | ||||||||||||||||||||||||
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 |