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- PDB-7lp4: Structure of Nedd4L WW3 domain -

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Basic information

Entry
Database: PDB / ID: 7lp4
TitleStructure of Nedd4L WW3 domain
ComponentsE3 ubiquitin-protein ligase NEDD4-like
KeywordsLIGASE / PPxY binding / E3 Ubiquitin ligase / Nedd4L
Function / homology
Function and homology information


positive regulation of caveolin-mediated endocytosis / negative regulation of sodium ion transmembrane transport / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of potassium ion transmembrane transporter activity / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium 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 sodium ion transmembrane transport ...positive regulation of caveolin-mediated endocytosis / negative regulation of sodium ion transmembrane transport / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of potassium ion transmembrane transporter activity / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium 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 sodium ion transmembrane transport / regulation of membrane depolarization / positive regulation of dendrite extension / potassium channel inhibitor activity / HECT-type E3 ubiquitin transferase / ventricular cardiac muscle cell action potential / regulation of monoatomic ion transmembrane transport / sodium channel inhibitor activity / regulation of dendrite morphogenesis / protein monoubiquitination / sodium channel regulator activity / potassium channel regulator activity / protein K48-linked ubiquitination / multivesicular body / regulation of membrane potential / Downregulation of TGF-beta receptor signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / regulation of protein stability / Budding and maturation of HIV virion / Stimuli-sensing channels / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / monoatomic ion transmembrane transport / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / cell differentiation / protein ubiquitination / Golgi apparatus / extracellular exosome / nucleoplasm / 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-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsAlam, S.L. / Alian, A. / Thompson, T. / Rheinemann, L. / Volkman, B.F. / Peterson, F.C. / Sundquist, W.I.
CitationJournal: 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
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4-like


Theoretical massNumber of molelcules
Total (without water)5,6061
Polymers5,6061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4-like / HECT-type E3 ubiquitin transferase NED4L / NEDD4.2 / Nedd4-2


Mass: 5606.483 Da / Num. of mol.: 1 / Fragment: WW 3 domain, residues 493-539
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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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
121isotropic12D 1H-15N HSQC
131isotropic12D 1H-13C HSQC aromatic
141isotropic12D 1H-13C HSQC aliphatic
151isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
171isotropic13D H(CCO)NH
181isotropic13D (H)CCH-TOCSY
191isotropic13D HNCO
1101anisotropic13D HN(CO)CA
1111isotropic13D HNCA
1121isotropic13D HNHA
1131isotropic13D HNHB
1141isotropic13D C(CO)NH
1151isotropic13D 1H-15N NOESY
1161isotropic33D 1H-15N NOESY
1171isotropic13D 1H-13C NOESY aliphatic
1181isotropic33D 1H-13C NOESY aliphatic
1191isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] E3 ubiquitin-protein ligase NEDD4-like, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O13C/15N_sample90% H2O/10% D2O
solution21 mM [U-100% 15N] E3 ubiquitin-protein ligase NEDD4-like, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mME3 ubiquitin-protein ligase NEDD4-like[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1 mME3 ubiquitin-protein ligase NEDD4-like[U-100% 15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 50 mM / Label: apo / pH: 7.5 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Felix2007Accelrys Software Inc.data analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing1
molecular dynamics6
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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