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- PDB-2ez5: Solution Structure of the dNedd4 WW3* Domain- Comm LPSY Peptide C... -

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Basic information

Entry
Database: PDB / ID: 2ez5
TitleSolution Structure of the dNedd4 WW3* Domain- Comm LPSY Peptide Complex
Components
  • Commissureless LPSY Peptide
  • E3 ubiquitin-protein ligase NEDD4
KeywordsSIGNALLING PROTEIN / LIGASE / Nedd4 / WW domain / Commissureless / PY motif / binding affinity
Function / homology
Function and homology information


positive regulation of cardiac myofibril assembly / dendrite guidance / subsynaptic reticulum / Downregulation of SMAD2/3:SMAD4 transcriptional activity / ISG15 antiviral mechanism / Downregulation of ERBB4 signaling / Regulation of PTEN localization / imaginal disc-derived wing vein morphogenesis / Roundabout binding / Antigen processing: Ubiquitination & Proteasome degradation ...positive regulation of cardiac myofibril assembly / dendrite guidance / subsynaptic reticulum / Downregulation of SMAD2/3:SMAD4 transcriptional activity / ISG15 antiviral mechanism / Downregulation of ERBB4 signaling / Regulation of PTEN localization / imaginal disc-derived wing vein morphogenesis / Roundabout binding / Antigen processing: Ubiquitination & Proteasome degradation / Regulation of PTEN stability and activity / neuron recognition / regulation of dendrite development / Golgi to lysosome transport / negative regulation of sodium ion transmembrane transporter activity / WW domain binding / positive regulation of cardioblast proliferation / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / axon midline choice point recognition / Notch binding / positive regulation of synapse assembly / dendrite morphogenesis / neuromuscular junction development / regulation of dendrite morphogenesis / myosin binding / negative regulation of Notch signaling pathway / positive regulation of endocytosis / positive regulation of receptor internalization / endocytic vesicle / negative regulation of smoothened signaling pathway / Notch signaling pathway / synapse assembly / axon guidance / cytoplasmic vesicle membrane / receptor internalization / protein polyubiquitination / endocytosis / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / late endosome / late endosome membrane / nervous system development / proteasome-mediated ubiquitin-dependent protein catabolic process / vesicle / membrane => GO:0016020 / protein ubiquitination / lysosomal membrane / protein domain specific binding / Golgi apparatus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Commissureless / Commissureless / E3 ubiquitin-protein ligase, SMURF1 type / 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 ...Commissureless / Commissureless / E3 ubiquitin-protein ligase, SMURF1 type / 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 / 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
Protein commissureless 1 / E3 ubiquitin-protein ligase Nedd-4
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKanelis, V. / Bruce, M.C. / Skrynnikov, N.R. / Rotin, D. / Forman-Kay, J.D.
CitationJournal: Structure / Year: 2006
Title: Structural Determinants for High-Affinity Binding in a Nedd4 WW3(*) Domain-Comm PY Motif Complex
Authors: Kanelis, V. / Bruce, M.C. / Skrynnikov, N.R. / Rotin, D. / Forman-Kay, J.D.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
W: E3 ubiquitin-protein ligase NEDD4
P: Commissureless LPSY Peptide


Theoretical massNumber of molelcules
Total (without water)6,3592
Polymers6,3592
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4 / E.C.6.3.2.- / DNedd4


Mass: 5155.705 Da / Num. of mol.: 1 / Fragment: WW3* domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9VVI3, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Commissureless LPSY Peptide


Mass: 1203.279 Da / Num. of mol.: 1 / Fragment: residues 227-237 / Source method: obtained synthetically
Details: A peptide comprising residues 227-237 of Commissureless from Drosophila melanogaster was made using standard Fmoc peptide synthesis
References: UniProt: Q24139

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N
12113C-EDITED NOESY
1313D F1-13C
14115N FILTERED NOESY
1512D F1-13C
16115N F2-13C
17115N FILTERED NOESY
NMR detailsText: MIXING TIMES WERE: 175 MS FOR THE 3D F1,F3-13C,15N EDITED NOESY; 140 FOR THE DOUBLE FILTERED NOESY; 250 FOR THE HALF-FILTERED NOESY

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Sample preparation

DetailsContents: 1.1 MM DNEDD4 WW3* DOMAIN, U- 13C,U-15N, 1.1 MM COMM LPSY PEPTIDE, UNLABELLED, 10 MM NA PHOS, PH 7.0, 20 MM NACL,90% H2O/10% D2O; 1.1 MM DNEDD4 WW3* DOMAIN, U- 13C,U -15N, 1.1 MM COMM LPSY ...Contents: 1.1 MM DNEDD4 WW3* DOMAIN, U- 13C,U-15N, 1.1 MM COMM LPSY PEPTIDE, UNLABELLED, 10 MM NA PHOS, PH 7.0, 20 MM NACL,90% H2O/10% D2O; 1.1 MM DNEDD4 WW3* DOMAIN, U- 13C,U -15N, 1.1 MM COMM LPSY PEPTIDE, UNLABELLED, 10 MM NA PHOS, PH 7.0, 20 MM NACL,100% D2O; 1.4 MM DNEDD4 WW3* DOMAIN, U- 13C,U -15N, 1.0 MM COMM LPSY PEPTIDE, UNLABELLED, 10 MM NA PHOS, PH 7.0, 20 MM NACL, 90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM NA PHOS, 20 mM NACL mM NA PHOS, 20 mM NACL; 10 mM NA PHOS, 20 mM NACL
pH: 7.0 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1NILGES, M.refinement
NMRPipe2.3structure solution
NMRView5.2.2structure solution
ARIA1structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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