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Yorodumi- PDB-1x5r: Solution structure of the fourth PDZ domain of Glutamate receptor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x5r | ||||||
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Title | Solution structure of the fourth PDZ domain of Glutamate receptor interacting protein 2 | ||||||
Components | Glutamate receptor interacting protein 2 | ||||||
Keywords | SIGNALING PROTEIN / PDZ domain / Glutamate receptor interacting protein 2 / GRIP2 protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information vesicle-mediated transport in synapse / Trafficking of GluR2-containing AMPA receptors / artery smooth muscle contraction / neurotransmitter receptor transport, endosome to postsynaptic membrane / neuron spine / positive regulation of blood pressure / glutamate receptor binding / postsynaptic density, intracellular component / Notch signaling pathway / postsynaptic membrane ...vesicle-mediated transport in synapse / Trafficking of GluR2-containing AMPA receptors / artery smooth muscle contraction / neurotransmitter receptor transport, endosome to postsynaptic membrane / neuron spine / positive regulation of blood pressure / glutamate receptor binding / postsynaptic density, intracellular component / Notch signaling pathway / postsynaptic membrane / neuronal cell body / glutamatergic synapse / dendrite / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the fourth PDZ domain of Glutamate receptor interacting protein 2 Authors: Qin, X.R. / 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 | 1x5r.cif.gz | 609.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x5r.ent.gz | 511.2 KB | Display | PDB format |
PDBx/mmJSON format | 1x5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/1x5r ftp://data.pdbj.org/pub/pdb/validation_reports/x5/1x5r | 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: 11449.641 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 pf00330s1 / Plasmid: P040705-16 / References: UniProt: Q9C0E4 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: spectrometer_id 1 for 3D_15N_separated_NOESY; spectrometer_id 2 for 3D_13C_separated_NOESY |
-Sample preparation
Details | Contents: 0.95mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-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: target function,structures with the lowest energy,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |