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Yorodumi- PDB-1um7: Solution structure of the third PDZ domain of synapse-associated ... -
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-Basic information
Entry | Database: PDB / ID: 1um7 | ||||||
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Title | Solution structure of the third PDZ domain of synapse-associated protein 102 | ||||||
Components | synapse-associated protein 102 | ||||||
Keywords | PROTEIN BINDING / PDZ / Discs large homolog 3 / DLG3-HUMAN presynaptic protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information establishment of planar polarity / NrCAM interactions / embryo development / receptor localization to synapse / Synaptic adhesion-like molecules / Assembly and cell surface presentation of NMDA receptors / establishment or maintenance of epithelial cell apical/basal polarity / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / Negative regulation of NMDA receptor-mediated neuronal transmission ...establishment of planar polarity / NrCAM interactions / embryo development / receptor localization to synapse / Synaptic adhesion-like molecules / Assembly and cell surface presentation of NMDA receptors / establishment or maintenance of epithelial cell apical/basal polarity / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane neurotransmitter receptor levels / receptor clustering / AMPA glutamate receptor complex / Long-term potentiation / positive regulation of protein tyrosine kinase activity / bicellular tight junction / phosphatase binding / Ras activation upon Ca2+ influx through NMDA receptor / adherens junction / postsynaptic density membrane / neuromuscular junction / kinase binding / cell-cell adhesion / RAF/MAP kinase cascade / chemical synaptic transmission / basolateral plasma membrane / neuron projection / negative regulation of cell population proliferation / glutamatergic synapse / ubiquitin protein ligase binding / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.-R. / Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the third PDZ domain of synapse-associated protein 102 Authors: Qin, X.-R. / Nagashima, T. / 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 | 1um7.cif.gz | 628.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1um7.ent.gz | 526.8 KB | Display | PDB format |
PDBx/mmJSON format | 1um7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1um7_validation.pdf.gz | 343.2 KB | Display | wwPDB validaton report |
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Full document | 1um7_full_validation.pdf.gz | 512.5 KB | Display | |
Data in XML | 1um7_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 1um7_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/1um7 ftp://data.pdbj.org/pub/pdb/validation_reports/um/1um7 | 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: 11654.825 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 / Gene: Kazusa cDNA KIAA1232 / Plasmid: P021030-42 / References: UniProt: Q92796 |
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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: 1.05mM 13C, 15N-labeled protein; 20mM phosphate buffer; 100mM NaCl; 1mM d10-DTT; 0.02% NaN3 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / 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, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |