+Open data
-Basic information
Entry | Database: PDB / ID: 7lp1 | ||||||
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Title | Structure of Nedd4L WW3 domain | ||||||
Components | E3 ubiquitin-protein ligase NEDD4-like | ||||||
Keywords | LIGASE / PPxY binding / E3 Ubiquitin ligase / Nedd4L | ||||||
Function / homology | Function and homology information 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 / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization ...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 / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization / regulation of membrane depolarization / positive regulation of dendrite extension / ventricular cardiac muscle cell action potential / potassium channel inhibitor activity / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / regulation of monoatomic ion transmembrane transport / regulation of dendrite morphogenesis / protein monoubiquitination / potassium channel regulator activity / sodium channel regulator activity / protein K48-linked ubiquitination / monoatomic ion transmembrane transport / multivesicular body / Downregulation of TGF-beta receptor signaling / regulation of membrane potential / Downregulation of SMAD2/3:SMAD4 transcriptional activity / regulation of protein stability / Budding and maturation of HIV virion / Stimuli-sensing channels / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / cell differentiation / protein ubiquitination / Golgi apparatus / extracellular exosome / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 | 7lp1.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lp1.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lp1_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 7lp1_full_validation.pdf.gz | 428.1 KB | Display | |
Data in XML | 7lp1_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 7lp1_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/7lp1 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/7lp1 | HTTPS FTP |
-Related structure data
Related structure data | 7lp2C 7lp3C 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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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4638.264 Da / Num. of mol.: 1 / Fragment: WW 3 domain, residues 494-532 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 | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.73 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 3.6M ammonium nitrate, 5% glycerol, and 0.1M sodium acetate at pH 4.6 |
-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: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 11774 / % possible obs: 99.83 % / Redundancy: 2 % / Biso Wilson estimate: 13 Å2 / CC1/2: 1 / Net I/σ(I): 33.25 |
Reflection shell | Resolution: 1.35→1.398 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1685 / Mean I/σ(I) obs: 4.26 / Num. unique obs: 1140 / CC1/2: 0.958 / Rrim(I) all: 0.2383 / % possible all: 98.16 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2mpt Resolution: 1.35→29.47 Å / SU ML: 0.095 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5887 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: 20.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→29.47 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 / Auth asym-ID: A / Label asym-ID: A
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