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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 / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Regulation of gap junction activity / positive regulation of cell communication by chemical coupling / Gap junction assembly / Downregulation of ERBB4 signaling / Regulation of PTEN localization / ISG15 antiviral mechanism / positive regulation of glomerular filtration / positive regulation of nucleocytoplasmic transport ...vascular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Regulation of gap junction activity / positive regulation of cell communication by chemical coupling / Gap junction assembly / Downregulation of ERBB4 signaling / Regulation of PTEN localization / ISG15 antiviral mechanism / positive regulation of glomerular filtration / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / RHOQ GTPase cycle / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of gonadotropin secretion / positive regulation of striated muscle tissue development / milk ejection reflex / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / positive regulation of behavioral fear response / chronic inflammatory response / Gap junction degradation / Formation of annular gap junctions / maintenance of protein localization in endoplasmic reticulum / columnar/cuboidal epithelial cell maturation / positive regulation of establishment of Sertoli cell barrier / negative regulation of sodium ion transport / neuroblast migration / regulation of cell communication by electrical coupling / negative regulation of trophoblast cell migration / endocardial cushion development / monoatomic ion transmembrane transporter activity / microtubule-based transport / gap junction hemi-channel activity / ATP transport / response to denervation involved in regulation of muscle adaptation / regulation of bone remodeling / nuclear receptor-mediated glucocorticoid signaling pathway / contractile muscle fiber / gap junction channel activity involved in cell communication by electrical coupling / regulation of ventricular cardiac muscle cell membrane depolarization / epididymis development / positive regulation of meiotic nuclear division / glutathione transmembrane transporter activity / endothelium development / gap junction assembly / cellular response to pH / negative regulation of cardiac muscle cell proliferation / regulation protein catabolic process at postsynapse / phosphothreonine residue binding / cardiac conduction / regulation of atrial cardiac muscle cell membrane depolarization / receptor catabolic process / regulation of actin filament organization / response to fluid shear stress / connexin complex / fascia adherens / Golgi-associated vesicle membrane / cell-cell contact zone / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein targeting to lysosome / gap junction / negative regulation of DNA biosynthetic process / skeletal muscle tissue regeneration / bone remodeling / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / gap junction channel activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / cell-cell junction organization / export across plasma membrane / regulation of bone mineralization / connexin binding / adult heart development / embryonic heart tube development / regulation of ventricular cardiac muscle cell membrane repolarization / tight junction / response to pH / sodium channel inhibitor activity / proline-rich region binding / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / glutamate secretion / RNA polymerase binding / blood vessel morphogenesis / beta-2 adrenergic receptor binding / lens development in camera-type eye / xenobiotic transport / intermediate filament / lysosomal transport / embryonic digit morphogenesis / sodium ion transport / regulation of dendrite morphogenesis / neuromuscular junction development / regulation of heart contraction / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of synapse organization / regulation of postsynaptic neurotransmitter receptor internalization
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 / 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
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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