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- PDB-2n8t: Solution Structure of the rNedd4 WW2 Domain-Cx43CT Peptide Comple... -

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Basic information

Entry
Database: PDB / ID: 2n8t
TitleSolution Structure of the rNedd4 WW2 Domain-Cx43CT Peptide Complex by NMR
Components
  • Cx43CT Peptide
  • E3 ubiquitin-protein ligase NEDD4
KeywordsLIGASE/peptide / rNedd4 WW2 / Cx43CT / phosphorylation / LIGASE / LIGASE-peptide complex
Function / homology
Function and homology information


vascular transport / positive regulation of striated muscle tissue development / milk ejection reflex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Regulation of gap junction activity / atrial ventricular junction remodeling / positive regulation of cell communication by chemical coupling / Gap junction assembly / cell communication by chemical coupling / Downregulation of ERBB4 signaling ...vascular transport / positive regulation of striated muscle tissue development / milk ejection reflex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Regulation of gap junction activity / atrial ventricular junction remodeling / positive regulation of cell communication by chemical coupling / Gap junction assembly / cell communication by chemical coupling / Downregulation of ERBB4 signaling / Regulation of PTEN localization / ISG15 antiviral mechanism / epididymis development / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / positive regulation of glomerular filtration / RHOQ GTPase cycle / Antigen processing: Ubiquitination & Proteasome degradation / neuroblast migration / columnar/cuboidal epithelial cell maturation / positive regulation of behavioral fear response / negative regulation of gonadotropin secretion / positive regulation of smooth muscle cell chemotaxis / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / regulation of bone remodeling / cell communication by electrical coupling / chronic inflammatory response / regulation of ventricular cardiac muscle cell membrane depolarization / contractile muscle fiber / negative regulation of DNA biosynthetic process / maintenance of protein localization in endoplasmic reticulum / Gap junction degradation / Formation of annular gap junctions / negative regulation of sodium ion transport / nuclear receptor-mediated glucocorticoid signaling pathway / channel inhibitor activity / regulation of cell communication by electrical coupling / response to denervation involved in regulation of muscle adaptation / negative regulation of trophoblast cell migration / endocardial cushion development / gap junction channel activity involved in cell communication by electrical coupling / microtubule-based transport / negative regulation of potassium ion export across plasma membrane / monoatomic ion transmembrane transporter activity / gap junction hemi-channel activity / ATP transport / positive regulation of establishment of Sertoli cell barrier / positive regulation of meiotic nuclear division / endothelium development / negative regulation of cardiac muscle cell proliferation / regulation of atrial cardiac muscle cell membrane depolarization / gap junction assembly / regulation protein catabolic process at postsynapse / fascia adherens / glutathione transmembrane transporter activity / cellular response to pH / cardiac conduction / regulation of actin filament organization / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / receptor catabolic process / cell-cell contact zone / phosphothreonine residue binding / protein targeting to lysosome / Golgi-associated vesicle membrane / connexin complex / potassium channel inhibitor activity / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / skeletal muscle tissue regeneration / response to fluid shear stress / regulation of bone mineralization / connexin binding / gap junction / bone remodeling / regulation of ventricular cardiac muscle cell membrane repolarization / HECT-type E3 ubiquitin transferase / export across plasma membrane / adult heart development / cell-cell junction organization / sodium channel inhibitor activity / embryonic heart tube development / proline-rich region binding / gap junction channel activity / response to pH / RNA polymerase binding / blood vessel morphogenesis / glutamate secretion / lens development in camera-type eye / intermediate filament / beta-2 adrenergic receptor binding / lysosomal transport / tight junction / embryonic digit morphogenesis / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of dendrite morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of stem cell proliferation / regulation of synapse organization
Similarity search - Function
Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / E3 ubiquitin-protein ligase, SMURF1 type / : / Connexin / Connexin, N-terminal / Connexin, conserved site ...Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / E3 ubiquitin-protein ligase, SMURF1 type / : / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain / 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
Gap junction alpha-1 protein / E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsSpagnol, G. / Kieken, F. / Sorgen, P.L.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structural Studies of the Nedd4 WW Domains and Their Selectivity for the Connexin43 (Cx43) Carboxyl Terminus.
Authors: Spagnol, G. / Kieken, F. / Kopanic, J.L. / Li, H. / Zach, S. / Stauch, K.L. / Grosely, R. / Sorgen, P.L.
History
DepositionOct 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4
B: Cx43CT Peptide


Theoretical massNumber of molelcules
Total (without water)6,0532
Polymers6,0532
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)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4


Mass: 4435.713 Da / Num. of mol.: 1 / Fragment: WW2 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nedd4, Nedd4a / Production host: Escherichia coli (E. coli)
References: UniProt: Q62940, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Cx43CT Peptide / Connexin-43 / Cx43 / Gap junction 43 kDa heart protein


Mass: 1617.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized, purchased from a vendor / References: UniProt: P08050
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNHA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.6 mM [U-98% 13C; U-98% 15N] rNedd4 WW2, 13 mM Cx43CT peptide, 1.8 mM potassium phosphate, 1 mM DTT, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMrNedd4 WW2-1[U-98% 13C; U-98% 15N]1
13 mMCx43CT peptide-21
1.8 mMpotassium phosphate-31
1 mMDTT-41
137 mMsodium chloride-51
2.7 mMpotassium chloride-61
10 mMsodium phosphate-71
Sample conditionsIonic strength: 156 / pH: 7.5 / Pressure: ambient / Temperature: 25 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.1Dr. Michael Nilges, Institut Pasteurrefinement
ARIA1.1Dr. Michael Nilges, Institut Pasteurgeometry optimization
ARIA1.1Dr. Michael Nilges, Institut Pasteurstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
NMRDrawF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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