+Open data
-Basic information
Entry | Database: PDB / ID: 2n8s | ||||||
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Title | Solution Structure of the rNedd4 WW1 Domain by NMR | ||||||
Components | E3 ubiquitin-protein ligase NEDD4 | ||||||
Keywords | LIGASE / rNedd4 WW1 | ||||||
Function / homology | Function and homology information Downregulation of ERBB4 signaling / Regulation of PTEN localization / ISG15 antiviral mechanism / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / endocardial cushion development / negative regulation of sodium ion transport / response to denervation involved in regulation of muscle adaptation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission ...Downregulation of ERBB4 signaling / Regulation of PTEN localization / ISG15 antiviral mechanism / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / endocardial cushion development / negative regulation of sodium ion transport / response to denervation involved in regulation of muscle adaptation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / intracellular glucocorticoid receptor signaling pathway / regulation protein catabolic process at postsynapse / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / regulation of postsynaptic neurotransmitter receptor internalization / proline-rich region binding / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / blood vessel morphogenesis / lysosomal transport / beta-2 adrenergic receptor binding / postsynaptic cytosol / neuromuscular junction development / regulation of dendrite morphogenesis / regulation of synapse organization / sodium ion transport / negative regulation of vascular endothelial growth factor receptor signaling pathway / outflow tract morphogenesis / protein monoubiquitination / progesterone receptor signaling pathway / microvillus / protein K63-linked ubiquitination / phosphoserine residue binding / ubiquitin ligase complex / ionotropic glutamate receptor binding / T cell activation / ubiquitin binding / regulation of membrane potential / establishment of localization in cell / receptor internalization / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / cellular response to UV / neuron projection development / ubiquitin protein ligase activity / cell cortex / ubiquitin-dependent protein catabolic process / adaptive immune response / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / immune response / protein domain specific binding / innate immune response / glutamatergic synapse / DNA damage response / chromatin / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Spagnol, G. / Kieken, F. / Sorgen, P.L. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2016 Title: Structural Studies of the Nedd4 WW Domains and Their Selectivity for the Connexin43 (Cx43) Carboxyl Terminus. Authors: Spagnol, G. / Kieken, F. / Kopanic, J.L. / Li, H. / Zach, S. / Stauch, K.L. / Grosely, R. / Sorgen, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n8s.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n8s.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 2n8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/2n8s ftp://data.pdbj.org/pub/pdb/validation_reports/n8/2n8s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4559.918 Da / Num. of mol.: 1 / Fragment: WW1 Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nedd4, Nedd4a / Production host: Escherichia coli (E. coli) References: UniProt: Q62940, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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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 mM [U-98% 13C; U-98% 15N] Nedd4 WW1, 1.8 mM potassium phosphate, 1 mM DTT, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 156 / pH: 7.5 / Pressure: ambient / Temperature: 25 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 10 |