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Yorodumi- PDB-1wf8: Solution structure of the PDZ domain of Spinophilin/NeurabinII protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wf8 | ||||||
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Title | Solution structure of the PDZ domain of Spinophilin/NeurabinII protein | ||||||
Components | Neurabin-I | ||||||
Keywords | PROTEIN BINDING / PDZ domain / Spinophilin/NeurabinII protein / STRUCTURAL GENOMICS / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information growth cone lamellipodium / regulation of synapse structural plasticity / negative regulation of spontaneous neurotransmitter secretion / positive regulation of long-term synaptic depression / : / : / cellular response to toxic substance / postsynaptic actin cytoskeleton organization / postsynaptic actin cytoskeleton / protein phosphatase 1 binding ...growth cone lamellipodium / regulation of synapse structural plasticity / negative regulation of spontaneous neurotransmitter secretion / positive regulation of long-term synaptic depression / : / : / cellular response to toxic substance / postsynaptic actin cytoskeleton organization / postsynaptic actin cytoskeleton / protein phosphatase 1 binding / regulation of filopodium assembly / regulation of actin filament polymerization / regulation of dendritic spine morphogenesis / negative regulation of stress fiber assembly / regulation of synapse assembly / cortical actin cytoskeleton / positive regulation of dendritic spine development / dendritic spine neck / negative regulation of long-term synaptic potentiation / positive regulation of protein kinase activity / excitatory postsynaptic potential / filopodium / calcium-mediated signaling / actin filament organization / neuromuscular junction / positive regulation of neuron projection development / neuron projection development / actin filament binding / actin cytoskeleton / GTPase binding / transmembrane transporter binding / postsynaptic density / protein domain specific binding / neuronal cell body / glutamatergic synapse / dendrite / protein kinase binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PDZ domain of Spinophilin/NeurabinII protein Authors: Qin, X. / 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 | 1wf8.cif.gz | 597.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wf8.ent.gz | 500.6 KB | Display | PDB format |
PDBx/mmJSON format | 1wf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wf8_validation.pdf.gz | 343.8 KB | Display | wwPDB validaton report |
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Full document | 1wf8_full_validation.pdf.gz | 502.9 KB | Display | |
Data in XML | 1wf8_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 1wf8_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/1wf8 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/1wf8 | 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: 10953.249 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 cNDA fh03567 / Plasmid: P021030-40 / References: UniProt: Q9ULJ8 |
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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 PiNa(pH6.0); 100mM NaCl; 1mM d-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, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |