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- PDB-2n8s: Solution Structure of the rNedd4 WW1 Domain by NMR -

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Basic information

Entry
Database: PDB / ID: 2n8s
TitleSolution Structure of the rNedd4 WW1 Domain by NMR
ComponentsE3 ubiquitin-protein ligase NEDD4
KeywordsLIGASE / rNedd4 WW1
Function / homology
Function and homology information


Downregulation of ERBB4 signaling / Regulation of PTEN localization / ISG15 antiviral mechanism / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of sodium ion transport / endocardial cushion development / response to denervation involved in regulation of muscle adaptation / nuclear receptor-mediated glucocorticoid signaling pathway ...Downregulation of ERBB4 signaling / Regulation of PTEN localization / ISG15 antiviral mechanism / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of sodium ion transport / endocardial cushion development / response to denervation involved in regulation of muscle adaptation / nuclear receptor-mediated glucocorticoid signaling pathway / phosphothreonine residue binding / receptor catabolic process / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / regulation protein catabolic process at postsynapse / protein targeting to lysosome / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / proline-rich region binding / sodium channel inhibitor activity / RNA polymerase binding / beta-2 adrenergic receptor binding / blood vessel morphogenesis / lysosomal transport / sodium ion transport / regulation of dendrite morphogenesis / neuromuscular junction development / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of synapse organization / regulation of postsynaptic neurotransmitter receptor internalization / outflow tract morphogenesis / microvillus / postsynaptic cytosol / phosphoserine residue binding / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / progesterone receptor signaling pathway / ionotropic glutamate receptor binding / T cell activation / ubiquitin binding / regulation of membrane potential / establishment of localization in cell / receptor internalization / positive regulation of protein catabolic process / neuron projection development / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / cell cortex / ubiquitin-dependent protein catabolic process / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / immune response / protein domain specific binding / innate immune response / DNA damage response / chromatin / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain ...E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsSpagnol, G. / Kieken, F. / Sorgen, P.L.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structural Studies of the Nedd4 WW Domains and Their Selectivity for the Connexin43 (Cx43) Carboxyl Terminus.
Authors: Spagnol, G. / Kieken, F. / Kopanic, J.L. / Li, H. / Zach, S. / Stauch, K.L. / Grosely, R. / Sorgen, P.L.
History
DepositionOct 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4


Theoretical massNumber of molelcules
Total (without water)4,5601
Polymers4,5601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4


Mass: 4559.918 Da / Num. of mol.: 1 / Fragment: WW1 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nedd4, Nedd4a / Production host: Escherichia coli (E. coli)
References: UniProt: Q62940, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNHA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] Nedd4 WW1, 1.8 mM potassium phosphate, 1 mM DTT, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNedd4 WW1-1[U-98% 13C; U-98% 15N]1
1.8 mMpotassium phosphate-21
1 mMDTT-31
137 mMsodium chloride-41
2.7 mMpotassium chloride-51
10 mMsodium phosphate-61
Sample conditionsIonic strength: 156 / pH: 7.5 / Pressure: ambient / Temperature: 25 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.1Dr. Michael Nilges, Institut Pasteurrefinement
ARIA1.1Dr. Michael Nilges, Institut Pasteurgeometry optimization
ARIA1.1Dr. Michael Nilges, Institut Pasteurstructure solution
NMRPipeF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
NMRDrawF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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