+Open data
-Basic information
Entry | Database: PDB / ID: 7lp3 | ||||||
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Title | Structure of Nedd4L WW3 domain | ||||||
Components |
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Keywords | LIGASE / PPxY binding / E3 Ubiquitin ligase / Nedd4L | ||||||
Function / homology | Function and homology information establishment of cell polarity involved in ameboidal cell migration / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / cell migration involved in gastrulation / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / positive regulation of embryonic development / Regulation of CDH11 function ...establishment of cell polarity involved in ameboidal cell migration / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / cell migration involved in gastrulation / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / positive regulation of embryonic development / Regulation of CDH11 function / regulation of sodium ion transmembrane transport / blood vessel endothelial cell migration / negative regulation of sodium ion transmembrane transporter activity / establishment of epithelial cell polarity / negative regulation of protein localization to cell surface / regulation of membrane repolarization / angiostatin binding / hippo signaling / positive regulation of dendrite extension / potassium channel inhibitor activity / ventricular cardiac muscle cell action potential / HECT-type E3 ubiquitin transferase / gastrulation with mouth forming second / negative regulation of vascular permeability / sodium channel inhibitor activity / regulation of monoatomic ion transmembrane transport / Signaling by Hippo / cell-cell junction assembly / regulation of small GTPase mediated signal transduction / regulation of dendrite morphogenesis / regulation of membrane depolarization / protein monoubiquitination / positive regulation of cell size / endocytic vesicle / sodium channel regulator activity / potassium channel regulator activity / bicellular tight junction / positive regulation of blood vessel endothelial cell migration / vasculogenesis / protein K48-linked ubiquitination / stress fiber / regulation of cell migration / positive regulation of stress fiber assembly / ruffle / monoatomic ion transmembrane transport / multivesicular body / negative regulation of angiogenesis / Downregulation of TGF-beta receptor signaling / regulation of membrane potential / actin filament / Downregulation of SMAD2/3:SMAD4 transcriptional activity / regulation of protein stability / Budding and maturation of HIV virion / protein localization / Stimuli-sensing channels / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / chemotaxis / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell junction / lamellipodium / signaling receptor activity / cytoplasmic vesicle / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / angiogenesis / in utero embryonic development / transmembrane transporter binding / cell differentiation / protein ubiquitination / external side of plasma membrane / Golgi apparatus / cell surface / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Alian, A. / Alam, S.L. / Thompson, T. / Rheinemann, L. / Sundquist, W.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Interactions between AMOT PPxY motifs and NEDD4L WW domains function in HIV-1 release. Authors: Rheinemann, L. / Thompson, T. / Mercenne, G. / Paine, E.L. / Peterson, F.C. / Volkman, B.F. / Alam, S.L. / Alian, A. / Sundquist, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lp3.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lp3.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 7lp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/7lp3 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/7lp3 | HTTPS FTP |
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-Related structure data
Related structure data | 7lp1C 7lp2C 7lp4C 7lp5C 2mptS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4445.951 Da / Num. of mol.: 2 / Fragment: WW 1 domain, residues 193-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q96PU5, HECT-type E3 ubiquitin transferase #2: Protein/peptide | Mass: 1644.869 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q4VCS5 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, sitting drop Details: 1.6M (NH4)2SO4, 0.1M Potassium Sodium Tartrate, 5% glycerol, 0.1M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→23.04 Å / Num. obs: 18091 / % possible obs: 99.19 % / Redundancy: 2 % / Biso Wilson estimate: 12.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0399 / Rrim(I) all: 0.0564 / Net I/σ(I): 7.05 |
Reflection shell | Resolution: 1.52→1.575 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6143 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1756 / CC1/2: 0.62 / Rrim(I) all: 0.8688 / % possible all: 96.03 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2mpt Resolution: 1.61→23.04 Å / SU ML: 0.1513 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8165 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 19.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→23.04 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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