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- PDB-1wr4: Solution structure of the second WW domain of Nedd4-2 -

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Basic information

Entry
Database: PDB / ID: 1wr4
TitleSolution structure of the second WW domain of Nedd4-2
Componentsubiquitin-protein ligase Nedd4-2
KeywordsLIGASE / all-beta
Function / homology
Function and homology information


Downregulation of SMAD2/3:SMAD4 transcriptional activity / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of sodium ion transport / negative regulation of sodium ion import across plasma membrane / negative regulation of potassium ion transmembrane transport / negative regulation of potassium ion export across plasma membrane / negative regulation of protein localization to cell surface / regulation protein catabolic process at postsynapse ...Downregulation of SMAD2/3:SMAD4 transcriptional activity / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of sodium ion transport / negative regulation of sodium ion import across plasma membrane / negative regulation of potassium ion transmembrane transport / negative regulation of potassium ion export across plasma membrane / negative regulation of protein localization to cell surface / regulation protein catabolic process at postsynapse / positive regulation of dendrite extension / regulation of membrane repolarization / positive regulation of sodium ion transport / receptor catabolic process / regulation of sodium ion transmembrane transport / Stimuli-sensing channels / potassium channel inhibitor activity / ventricular cardiac muscle cell action potential / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of systemic arterial blood pressure / sodium ion import across plasma membrane / regulation of bicellular tight junction assembly / regulation of membrane depolarization / regulation of dendrite morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / regulation of synapse organization / neuromuscular junction development / sodium channel regulator activity / protein monoubiquitination / protein K48-linked ubiquitination / regulation of sodium ion transport / response to salt stress / multivesicular body / regulation of membrane potential / regulation of protein stability / receptor internalization / neuron projection development / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / apical plasma membrane / postsynapse / protein ubiquitination / glutamatergic synapse / Golgi apparatus / 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 / C2 domain / C2 domain profile. / WW/rsp5/WWP domain signature. / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsKowalski, K. / Merkel, A.L. / Booker, G.W.
CitationJournal: To be Published
Title: Solution structures of the WW domains of Nedd4-2
Authors: Kowalski, K. / Merkel, A.L. / Booker, G.W.
History
DepositionOct 11, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ubiquitin-protein ligase Nedd4-2


Theoretical massNumber of molelcules
Total (without water)4,1851
Polymers4,1851
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ubiquitin-protein ligase Nedd4-2


Mass: 4184.633 Da / Num. of mol.: 1 / Fragment: second WW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8CFI0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1322D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM WW2; 100mM NaCl; 25mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM WW2; 100mM NaCl; 25mM phosphate buffer; 100% D2O100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.3Delaglio et alprocessing
Sparky3.1Goddard & Knellerdata analysis
ARIA1.2Linge et alstructure solution
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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