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- PDB-1i5h: SOLUTION STRUCTURE OF THE RNEDD4 WWIII DOMAIN-RENAL BP2 PEPTIDE C... -

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Basic information

Entry
Database: PDB / ID: 1i5h
TitleSOLUTION STRUCTURE OF THE RNEDD4 WWIII DOMAIN-RENAL BP2 PEPTIDE COMPLEX
Components
  • AMILORIDE-SENSITIVE SODIUM CHANNEL BETA-SUBUNIT
  • UBIQUITIN LIGASE NEDD4
KeywordsLIGASE / Nedd4 / WW domains / ENaC / PY Motif / Liddle syndrome / proline-rich
Function / homology
Function and homology information


Downregulation of ERBB4 signaling / Stimuli-sensing channels / Regulation of PTEN localization / ISG15 antiviral mechanism / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / sodium channel complex / ligand-gated sodium channel activity / endocardial cushion development ...Downregulation of ERBB4 signaling / Stimuli-sensing channels / Regulation of PTEN localization / ISG15 antiviral mechanism / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / sodium channel complex / ligand-gated sodium channel activity / endocardial cushion development / negative regulation of sodium ion transport / response to denervation involved in regulation of muscle adaptation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / nuclear receptor-mediated glucocorticoid signaling pathway / sodium ion homeostasis / artery smooth muscle contraction / regulation protein catabolic process at postsynapse / WW domain binding / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome / multicellular organismal-level water homeostasis / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / plasma membrane protein complex / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / regulation of postsynaptic neurotransmitter receptor internalization / proline-rich region binding / regulation of monoatomic ion transmembrane transport / wound healing, spreading of epidermal cells / RNA polymerase binding / blood vessel morphogenesis / postsynaptic cytosol / lysosomal transport / neuromuscular junction development / sodium ion transport / regulation of dendrite morphogenesis / regulation of synapse organization / negative regulation of vascular endothelial growth factor receptor signaling pathway / outflow tract morphogenesis / progesterone receptor signaling pathway / plasma membrane => GO:0005886 / protein monoubiquitination / microvillus / protein K63-linked ubiquitination / sodium ion transmembrane transport / phosphoserine residue binding / beta-2 adrenergic receptor binding / regulation of sodium ion transport / ubiquitin ligase complex / T cell activation / ubiquitin binding / establishment of localization in cell / regulation of membrane potential / ionotropic glutamate receptor binding / cytoplasmic vesicle membrane / receptor internalization / sensory perception of taste / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / cellular response to UV / neuron projection development / ubiquitin protein ligase activity / cell cortex / ubiquitin-dependent protein catabolic process / adaptive immune response / dendritic spine / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / protein ubiquitination / immune response / apical plasma membrane / protein domain specific binding / external side of plasma membrane / innate immune response / glutamatergic synapse / DNA damage response / chromatin / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / cell surface / protein-containing complex / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / E3 ubiquitin-protein ligase, SMURF1 type / 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 / E3 ubiquitin-protein ligase, SMURF1 type / 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 / 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 / Single Sheet / C2 domain superfamily / Mainly Beta
Similarity search - Domain/homology
Amiloride-sensitive sodium channel subunit beta / E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKanelis, V. / Rotin, D. / Forman-Kay, J.D.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Solution structure of a Nedd4 WW domain-ENaC peptide complex.
Authors: Kanelis, V. / Rotin, D. / Forman-Kay, J.D.
History
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
W: UBIQUITIN LIGASE NEDD4
B: AMILORIDE-SENSITIVE SODIUM CHANNEL BETA-SUBUNIT


Theoretical massNumber of molelcules
Total (without water)7,3922
Polymers7,3922
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 / 170structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide UBIQUITIN LIGASE NEDD4 / RNEDD4


Mass: 5666.237 Da / Num. of mol.: 1 / Fragment: WWIII DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62940
#2: Protein/peptide AMILORIDE-SENSITIVE SODIUM CHANNEL BETA-SUBUNIT / RENAL BP2 PEPTIDE


Mass: 1725.894 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: AN IDENTICAL PEPTIDE WAS MADE SYNTHETICALLY USING STANDARD F-MOC CHEMISTRY FOR NMR SAMPLES REQUIRING UNLABELED BP2 PEPTIDE.
Plasmid: PGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37090

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N/13C-edited NOESY
1233D 13C F1-filtered, F3-edited NOESY
1323D 15N/13C-edited NOESY
1443D 13C F1-filtered, F3-edited NOESY
152HN(CO)CA COHACA CROSS
162HN(CO)CA HNHA CROSS
171J-HNHA
182J-HNHA
191HNCO-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1Sample 1:1mM rNedd4 WWIII U-15N,13C; 3mM rENaC bP2 NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF; Sample 2:1mM rENaC bP2 U-15N,13C; 3mM rNedd4 WWIII NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF; MORE DETAILED DESCRIPTION GIVEN IN BMRB 496390% H2O/10% D2O
21mM rENaC bP2 U-15N,13C; 3mM rNedd4 WWIII NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF;90% H2O/10% D2O
31mM rNedd4 WWIII U-15N,13C; 3mM rENaC bP2 NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF;100% D2O
41mM rENaC bP2 U-15N,13C; 3mM rNedd4 WWIII NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF;100% D2O
Sample conditionsIonic strength: 0.01 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, A.processing
NMRVeiw4.1.2Johnson, B.A and Blevis, B.A.data analysis
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and warren, G.L.structure solution
ARIA1Nilges, M.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Preliminary structures were calculated using CNS1.0. These structures were then used as input into the program ARIA1.0 for noe assignment and structure refinement. These structures were ...Details: Preliminary structures were calculated using CNS1.0. These structures were then used as input into the program ARIA1.0 for noe assignment and structure refinement. These structures were calculated using 1799 unambiguous and 214 ambiguous NOEs, 14 hydrogen bond restraints, 44 dihedral angle restraints and directly refined against 33 Jhnha coupling constants.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 170 / Conformers submitted total number: 15

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