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- PDB-5aht: Third WW domain from the E3 ubiquitin-protein ligase NEDD4 -

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Basic information

Entry
Database: PDB / ID: 5aht
TitleThird WW domain from the E3 ubiquitin-protein ligase NEDD4
ComponentsE3 UBIQUITIN-PROTEIN LIGASE NEDD4
KeywordsISOMERASE / WW3 / PROTEIN-PEPTIDE COMPLEX / PROTEIN DYNAMICS / PROEIN STRUCTURE
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 / phosphothreonine residue binding / receptor catabolic process / 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 / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome / apicolateral plasma membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / proline-rich region binding / regulation of monoatomic ion transmembrane transport / 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 PTEN localization / ubiquitin binding / regulation of membrane potential / receptor internalization / ISG15 antiviral mechanism / Regulation of PTEN stability and activity / response to calcium ion / positive regulation of protein catabolic process / cellular response to UV / neuron projection development / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Single Sheet / C2 domain superfamily / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / SEMI-AUTOMATED NOE ASSIGNMENT, SIMULATED ANNEALING
AuthorsPanwalkar, V. / Lecher, J. / Dingley, A.
CitationJournal: Biochemistry / Year: 2016
Title: The Nedd4-1 Ww Domain Recognizes the Py Motif Peptide Through Coupled Folding and Binding Equilibria.
Authors: Panwalkar, V. / Neudecker, P. / Schmitz, M. / Lecher, J. / Schulte, M. / Medini, K. / Stoldt, M. / Brimble, M.A. / Willbold, D. / Dingley, A.J.
History
DepositionFeb 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 2.0Jun 23, 2021Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.field_strength
Revision 2.1Jan 31, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE NEDD4


Theoretical massNumber of molelcules
Total (without water)4,9721
Polymers4,9721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide E3 UBIQUITIN-PROTEIN LIGASE NEDD4


Mass: 4971.609 Da / Num. of mol.: 1 / Fragment: WW3, UNP RESIDUES 838-877
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX2TK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P46934, ubiquitin-protein ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C HSQCNOESY
12115N HSQCNOESY
13113C(AROMATIC) HSQCNOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED NEDD4 WW3.

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Sample preparation

Details
Solution-IDContents
11.5 MM [U-99% 13C
2U-99% 15N] NEDD4 WW3* DOMAIN, 20 MM SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE, 0.5 MM DSS, 90% 2O/10% D2O
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian VNMRSYS / Manufacturer: Varian / Model: VNMRSYS / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CcpNmr Analysis2.4.1structure solution
ARIA2.3.2structure solution
relax3.3.6structure solution
NMRPipestructure solution
RefinementMethod: SEMI-AUTOMATED NOE ASSIGNMENT, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 15

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