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- PDB-2m3o: Structure and dynamics of a human Nedd4 WW domain-ENaC complex -

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Basic information

Entry
Database: PDB / ID: 2m3o
TitleStructure and dynamics of a human Nedd4 WW domain-ENaC complex
Components
  • Amiloride-sensitive sodium channel subunit alpha
  • E3 ubiquitin-protein ligase NEDD4
KeywordsPEPTIDE BINDING PROTEIN/PROTEIN BINDING / WW domain / ENaC / Ubiquitin E3 ligase / PEPTIDE BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


sensory perception of salty taste / formation of structure involved in a symbiotic process / Sensory perception of salty taste / positive regulation of nucleocytoplasmic transport / sensory perception of sour taste / cellular response to vasopressin / sperm principal piece / sodium channel complex / negative regulation of sodium ion transport / ligand-gated sodium channel activity ...sensory perception of salty taste / formation of structure involved in a symbiotic process / Sensory perception of salty taste / positive regulation of nucleocytoplasmic transport / sensory perception of sour taste / cellular response to vasopressin / sperm principal piece / sodium channel complex / negative regulation of sodium ion transport / ligand-gated sodium channel activity / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / sodium ion homeostasis / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / cellular response to aldosterone / protein targeting to lysosome / apicolateral plasma membrane / multicellular organismal-level water homeostasis / cellular response to acidic pH / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / sodium ion import across plasma membrane / HECT-type E3 ubiquitin transferase / intracellular sodium ion homeostasis / regulation of monoatomic ion transmembrane transport / sodium channel inhibitor activity / motile cilium / proline-rich region binding / RNA polymerase binding / beta-2 adrenergic receptor binding / lysosomal transport / ciliary membrane / WW domain 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 / phosphoserine residue binding / regulation of macroautophagy / sodium ion transmembrane transport / progesterone receptor signaling pathway / ubiquitin ligase complex / Downregulation of ERBB4 signaling / Regulation of PTEN localization / acrosomal vesicle / regulation of membrane potential / ubiquitin binding / receptor internalization / Stimuli-sensing channels / ISG15 antiviral mechanism / regulation of blood pressure / 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 / apical plasma membrane / protein domain specific binding / external side of plasma membrane / innate immune response / DNA damage response / chromatin / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / HECT domain / HECT, E3 ligase catalytic domain ...Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel / 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
Amiloride-sensitive sodium channel subunit alpha / E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBobby, R. / Medini, K. / Neudecker, P. / Lee, V. / MacDonald, F.J. / Brimble, M.A. / Lott, J. / Dingley, A.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Structure and dynamics of human Nedd4-1 WW3 in complex with the alpha ENaC PY motif.
Authors: Bobby, R. / Medini, K. / Neudecker, P. / Lee, T.V. / Brimble, M.A. / McDonald, F.J. / Lott, J.S. / Dingley, A.J.
History
DepositionJan 23, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
W: E3 ubiquitin-protein ligase NEDD4
P: Amiloride-sensitive sodium channel subunit alpha


Theoretical massNumber of molelcules
Total (without water)6,0302
Polymers6,0302
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)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4 / Cell proliferation-inducing gene 53 protein / Neural precursor cell expressed developmentally down- ...Cell proliferation-inducing gene 53 protein / Neural precursor cell expressed developmentally down-regulated protein 4 / NEDD-4


Mass: 4971.609 Da / Num. of mol.: 1 / Fragment: third WW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4, KIAA0093, NEDD4-1, PIG53 / Plasmid: pET42 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)pLysS / References: UniProt: P46934
#2: Protein/peptide Amiloride-sensitive sodium channel subunit alpha / Alpha-NaCH / Epithelial Na(+) channel subunit alpha / Alpha-ENaC / ENaCA / Nonvoltage-gated sodium ...Alpha-NaCH / Epithelial Na(+) channel subunit alpha / Alpha-ENaC / ENaCA / Nonvoltage-gated sodium channel 1 subunit alpha / SCNEA


Mass: 1058.184 Da / Num. of mol.: 1 / Fragment: alpha ENaC PY peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P37088

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-15N TOCSY
11113D 1H-13C NOESY
11222D CBCA(CO)NH
11322D C(CO)NH
11422D HNCO
11522D HN(CA)CB
11623D (H)CCH-TOCSY
11723D 1H-15N NOESY
11823D 1H-15N TOCSY
11923D 1H-13C NOESY
12022D 1H-15N NOESY
12122D 1H-13C NOESY
12223D 15N/13C-EDITED NOESY
12322D 13C-edited/filtered NOESY
12412D long-range HNCO
12532D 1H-15N R2 relaxation
12632D 1H-15N R1 relaxation
12732D 1H-15N heteronuclear NOE
12832D 1H-15N R1rho relaxation
12932D 1H-15N R1 relaxation
13032D 1H-15N heteronuclear NOE
13132D 1H-15N R1rho relaxation
13232D 1H-15N R1 relaxation
13332D 1H-15N heteronuclear NOE
13413D HCAN
13522D HCAN
13612D (HB)CB(CGCD)HD
13712D (HB)CB(CGCDCE)HE
13822D HBCBCACONHAN
13922D HBCBCACONHACA
14032D 15N CPMG dispersion
14132D 15N CPMG dispersion

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-99% 13C; U-99% 15N] Nedd4 WW3* domain, 2.2 mM alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1 mM TSP, 93% H2O/7% D2O93% H2O/7% D2O
23.0 mM Nedd4 WW3* domain, 1.5 mM [U-99% 13C; U-99% 15N] alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1.0 mM TSP, 93% H2O/7% D2O93% H2O/7% D2O
31.61 mM [U-99% 15N] Nedd4 WW3* domain, 4.38 mM alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1 mM TSP, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMNedd4 WW3* domain-1[U-99% 13C; U-99% 15N]1
2.2 mMalpha ENaC PY peptide-21
20 mMsodium phosphate-31
0.1 %sodium azide-41
1 mMTSP-51
3.0 mMNedd4 WW3* domain-62
1.5 mMalpha ENaC PY peptide-7[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-82
0.1 %sodium azide-92
1.0 mMTSP-102
1.61 mMNedd4 WW3* domain-11[U-99% 15N]3
4.38 mMalpha ENaC PY peptide-123
20 mMsodium phosphate-133
0.1 %sodium azide-143
1 mMTSP-153
Sample conditionsIonic strength: 0.02 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian Direct DriveVarianDirect Drive8002
Varian Direct DriveVarianDirect Drive9003
Varian Unity INOVAVarianUnity INOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1pl3Bruker Biospincollection
CcpNMR2.07CCPNpeak picking
CcpNMR2.07CCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
relax2.0.0d'Auvergne, E. J. and Gooley, P. R.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT AGAINST DISTANCE, TORSION ANGLE AND RDC CONSTRAINTS IN A 8 ANGSTROM WATER SHELL, USING A MODIFIED VERSION OF THE WATERREFCNS SCRIPTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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