+Open data
-Basic information
Entry | Database: PDB / ID: 4n7f | ||||||
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Title | Crystal structure of 3rd WW domain of human Nedd4-1 | ||||||
Components | E3 ubiquitin-protein ligase NEDD4 | ||||||
Keywords | PROTEIN BINDING / beta sheet / WW domain / target binding / proline rich region / cytosolic | ||||||
Function / homology | Function and homology information formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / intracellular glucocorticoid receptor signaling pathway / negative regulation of sodium ion transmembrane transporter activity / receptor catabolic process / phosphothreonine residue binding / protein targeting to lysosome ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / intracellular glucocorticoid receptor signaling pathway / negative regulation of sodium ion transmembrane transporter activity / receptor catabolic process / phosphothreonine residue binding / protein targeting to lysosome / apicolateral plasma membrane / 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 / proline-rich region binding / RNA polymerase binding / lysosomal transport / beta-2 adrenergic receptor binding / 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 / phosphoserine residue binding / regulation of macroautophagy / ubiquitin ligase complex / Downregulation of ERBB4 signaling / regulation of membrane potential / Regulation of PTEN localization / ubiquitin binding / receptor internalization / ISG15 antiviral mechanism / 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 / protein domain specific binding / 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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.102 Å | ||||||
Authors | Qi, S. / O'Hayre, M. / Gutkind, J.S. / Hurley, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural and biochemical basis for ubiquitin ligase recruitment by arrestin-related domain-containing protein-3 (ARRDC3). Authors: Qi, S. / O'Hayre, M. / Gutkind, J.S. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n7f.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n7f.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 4n7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/4n7f ftp://data.pdbj.org/pub/pdb/validation_reports/n7/4n7f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4447.042 Da / Num. of mol.: 2 / Fragment: WW3 domain (UNP residues 841-874) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0093, NEDD4, NEDD4-1, PIG53 / Plasmid: pGST-parallel2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46934 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3.0M NaCl, 100mM Tris-HCl 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 21, 2012 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.1→32.7 Å / Num. all: 36280 / Num. obs: 36262 / % possible obs: 95 % | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.102→32.713 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8829 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 18.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 265.74 Å2 / Biso mean: 27.4254 Å2 / Biso min: 8.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.102→32.713 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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