+Open data
-Basic information
Entry | Database: PDB / ID: 2m3o | ||||||
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Title | Structure and dynamics of a human Nedd4 WW domain-ENaC complex | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN/PROTEIN BINDING / WW domain / ENaC / Ubiquitin E3 ligase / PEPTIDE BINDING PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information sensory perception of salty taste / formation of structure involved in a symbiotic process / Sensory perception of salty taste / positive regulation of nucleocytoplasmic transport / cellular response to vasopressin / sensory perception of sour taste / sodium channel complex / sperm principal piece / ligand-gated sodium channel activity / negative regulation of sodium ion transport ...sensory perception of salty taste / formation of structure involved in a symbiotic process / Sensory perception of salty taste / positive regulation of nucleocytoplasmic transport / cellular response to vasopressin / sensory perception of sour taste / sodium channel complex / sperm principal piece / ligand-gated sodium channel activity / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / intracellular glucocorticoid receptor signaling pathway / sodium ion homeostasis / negative regulation of sodium ion transmembrane transporter activity / WW domain binding / receptor catabolic process / phosphothreonine residue binding / cellular response to aldosterone / protein targeting to lysosome / cellular response to acidic pH / apicolateral plasma membrane / multicellular organismal-level water homeostasis / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / HECT-type E3 ubiquitin transferase / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of monoatomic ion transmembrane transport / sodium channel inhibitor activity / motile cilium / proline-rich region binding / RNA polymerase binding / lysosomal transport / beta-2 adrenergic receptor binding / ciliary membrane / neuromuscular junction development / regulation of dendrite morphogenesis / regulation of synapse organization / negative regulation of vascular endothelial growth factor receptor signaling pathway / protein K63-linked ubiquitination / progesterone receptor signaling pathway / sodium ion transmembrane transport / phosphoserine residue binding / regulation of macroautophagy / ubiquitin ligase complex / Downregulation of ERBB4 signaling / regulation of membrane potential / Regulation of PTEN localization / acrosomal vesicle / ubiquitin binding / Stimuli-sensing channels / receptor internalization / ISG15 antiviral mechanism / regulation of blood pressure / Regulation of PTEN stability and activity / response to calcium ion / neuron projection development / positive regulation of protein catabolic process / cellular response to UV / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell cortex / ubiquitin-dependent protein catabolic process / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / apical plasma membrane / protein domain specific binding / external side of plasma membrane / innate immune response / DNA damage response / chromatin / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Bobby, R. / Medini, K. / Neudecker, P. / Lee, V. / MacDonald, F.J. / Brimble, M.A. / Lott, J. / Dingley, A.J. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Structure and dynamics of human Nedd4-1 WW3 in complex with the alpha ENaC PY motif. Authors: Bobby, R. / Medini, K. / Neudecker, P. / Lee, T.V. / Brimble, M.A. / McDonald, F.J. / Lott, J.S. / Dingley, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m3o.cif.gz | 286 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m3o.ent.gz | 247.4 KB | Display | PDB format |
PDBx/mmJSON format | 2m3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/2m3o ftp://data.pdbj.org/pub/pdb/validation_reports/m3/2m3o | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4971.609 Da / Num. of mol.: 1 / Fragment: third WW domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4, KIAA0093, NEDD4-1, PIG53 / Plasmid: pET42 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)pLysS / References: UniProt: P46934 |
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#2: Protein/peptide | Mass: 1058.184 Da / Num. of mol.: 1 / Fragment: alpha ENaC PY peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P37088 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.02 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: REFINEMENT AGAINST DISTANCE, TORSION ANGLE AND RDC CONSTRAINTS IN A 8 ANGSTROM WATER SHELL, USING A MODIFIED VERSION OF THE WATERREFCNS SCRIPTS. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 15 |