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- PDB-6rss: Solution structure of the fourth WW domain of WWP2 with GB1-tag -

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Basic information

Entry
Database: PDB / ID: 6rss
TitleSolution structure of the fourth WW domain of WWP2 with GB1-tag
ComponentsNEDD4-like E3 ubiquitin-protein ligase WWP2
KeywordsPROTEIN BINDING / Three-stranded antiparallel beta-sheet / PPxY motif binding / E3 ubiquitin ligase / NEDD4
Function / homology
Function and homology information


negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / negative regulation of transporter activity / regulation of monoatomic ion transmembrane transport / negative regulation of Notch signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / protein K63-linked ubiquitination ...negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / negative regulation of transporter activity / regulation of monoatomic ion transmembrane transport / negative regulation of Notch signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / protein K63-linked ubiquitination / RHOU GTPase cycle / transcription factor binding / protein autoubiquitination / ubiquitin ligase complex / regulation of membrane potential / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein modification process / negative regulation of DNA-binding transcription factor activity / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein ubiquitination / symbiont entry into host cell / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / 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) / WW domain / WW/rsp5/WWP domain signature. / C2 domain ...E3 ubiquitin-protein ligase, SMURF1 type / 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) / 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
NEDD4-like E3 ubiquitin-protein ligase WWP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsWahl, L.C. / Watt, J.E. / Tolchard, J. / Blumenschein, T.M.A. / Chantry, A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Other private United Kingdom
Other private United Kingdom
Other private United Kingdom
Other private United Kingdom
CitationJournal: Int J Mol Sci / Year: 2019
Title: Smad7 Binds Differently to Individual and Tandem WW3 and WW4 Domains of WWP2 Ubiquitin Ligase Isoforms.
Authors: Wahl, L.C. / Watt, J.E. / Yim, H.T.T. / De Bourcier, D. / Tolchard, J. / Soond, S.M. / Blumenschein, T.M.A. / Chantry, A.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP2


Theoretical massNumber of molelcules
Total (without water)11,9741
Polymers11,9741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8570 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein NEDD4-like E3 ubiquitin-protein ligase WWP2 / Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain- ...Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain-containing protein 2


Mass: 11974.083 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP2 / Plasmid: pSKDuet01 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21 Star(DE3)
References: UniProt: O00308, HECT-type E3 ubiquitin transferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
171isotropic12D 1H-13C HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D H(CCO)NH
151isotropic13D C(CO)NH
182isotropic23D (H)CCH-TOCSY
1122isotropic23D CCH-TOCSY
1131isotropic12D 1H-13C TOCSY aromatic
1112isotropic22D (HB)CB(CGCD)HD
1102isotropic12D 1H-1H NOESY aromatic
161isotropic23D 1H-15N NOESY
191isotropic13D 1H-13C NOESY
1141isotropic12D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.2 mM [U-99% 13C; U-99% 15N] WWP2 WW4 domain, 90% H2O/10% D2O13C_15N_WWP2_WW490% H2O/10% D2O
solution22.08 mM [U-99% 13C; U-99% 15N] WWP2 WW4 domain, 90% H2O/10% D2O13C_15N_WWP2_WW490% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMWWP2 WW4 domain[U-99% 13C; U-99% 15N]1
2.08 mMWWP2 WW4 domain[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 110 mM / Label: Buffer / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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