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- PDB-7lp5: Structure of Nedd4L WW3 domain -

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Basic information

Entry
Database: PDB / ID: 7lp5
TitleStructure of Nedd4L WW3 domain
ComponentsAngiomotin,E3 ubiquitin-protein ligase NEDD4-like
KeywordsLIGASE / WW domain / 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 / Signaling by Hippo / regulation of monoatomic ion transmembrane transport / 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 / monoatomic ion transmembrane transport / ruffle / 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 / Budding and maturation of HIV virion / regulation of protein stability / 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
Angiomotin / Angiomotin, C-terminal / Angiomotin C terminal / 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 / C2 domain ...Angiomotin / Angiomotin, C-terminal / Angiomotin C terminal / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / 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
Angiomotin / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
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 1.2May 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,7571
Polymers7,7571
Non-polymers00
Water0
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 Angiomotin,E3 ubiquitin-protein ligase NEDD4-like / HECT-type E3 ubiquitin transferase NED4L / NEDD4.2 / Nedd4-2


Mass: 7756.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMOT, KIAA1071, NEDD4L, KIAA0439, NEDL3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q4VCS5, 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
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D C(CO)NH
161isotropic13D H(CCO)NH
171isotropic13D (H)CCH-TOCSY
181isotropic13D HNHB
191isotropic13D HNHA
1101isotropic13D CBCA(CO)NH
1111isotropic12D 1H-13C HSQC aliphatic
1121isotropic12D 1H-13C HSQC aromatic
1131isotropic23D 1H-15N NOESY
1141isotropic23D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aromatic

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Sample preparation

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

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Felix2007Accelrys Software Inc.data analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
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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