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- PDB-2mpt: WW3 domain of Nedd4L in complex with its HECT domain PY motif -

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Basic information

Entry
Database: PDB / ID: 2mpt
TitleWW3 domain of Nedd4L in complex with its HECT domain PY motif
Components(E3 ubiquitin-protein ligase NEDD4-like) x 2
KeywordsLIGASE / WW / Nedd4L / Nedd4.2 / HECT / PY / WW3 / Auto-ubiquitination / Proteasomal degradation / Ubiquitin ligase
Function / homology
Function and homology information


negative regulation of sodium ion import across plasma membrane / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / : / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization ...negative regulation of sodium ion import across plasma membrane / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / : / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization / regulation of sodium ion transmembrane transport / regulation of membrane depolarization / potassium channel inhibitor activity / receptor catabolic process / positive regulation of dendrite extension / ventricular cardiac muscle cell action potential / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / regulation of dendrite morphogenesis / neuromuscular junction development / regulation of synapse organization / sodium channel regulator activity / protein monoubiquitination / potassium channel regulator activity / protein K48-linked ubiquitination / multivesicular body / Downregulation of TGF-beta receptor signaling / regulation of membrane potential / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Budding and maturation of HIV virion / regulation of protein stability / receptor internalization / Stimuli-sensing channels / positive regulation of protein catabolic process / neuron projection development / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / monoatomic ion transmembrane transport / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination / apical plasma membrane / Golgi apparatus / extracellular exosome / nucleoplasm / 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) / C2 domain / WW 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) / 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
E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsEscobedo, A. / Macias, M.J. / Gomes, T. / Aragon, E. / Martin-Malpartida, P. / Ruiz, L.
CitationJournal: Structure / Year: 2014
Title: Structural Basis of the Activation and Degradation Mechanisms of the E3 Ubiquitin Ligase Nedd4L.
Authors: Escobedo, A. / Gomes, T. / Aragon, E. / Martin-Malpartida, P. / Ruiz, L. / Macias, M.J.
History
DepositionJun 2, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 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 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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-like
B: E3 ubiquitin-protein ligase NEDD4-like


Theoretical massNumber of molelcules
Total (without water)7,2722
Polymers7,2722
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)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4-like / NEDD4.2 / Nedd4-2


Mass: 5665.508 Da / Num. of mol.: 1 / Fragment: WW3 domain, UNP RESIDUES 496-539
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide E3 ubiquitin-protein ligase NEDD4-like / NEDD4.2 / Nedd4-2


Mass: 1606.774 Da / Num. of mol.: 1 / Fragment: HECT domain PY motif, UNP RESIDUES 945-957 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
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-1H NOESY
1212D 1H-1H TOCSY
1323D 1H-15N NOESY
1423D 1H-15N TOCSY
1533D HN(CA)CB
1633D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM WW3-1, 1.4 mM HECT_PY-2, 150 mM sodium chloride-3, 20 mM sodium phosphate-4, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] WW3-5, 2 mM HECT_PY-6, 150 mM sodium chloride-7, 20 mM sodium phosphate-8, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 13C; U-100% 15N] WW3-9, 1.6 mM HECT_PY-10, 150 mM sodium chloride-11, 20 mM sodium phosphate-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMWW3-11
1.4 mMHECT_PY-21
150 mMsodium chloride-31
20 mMsodium phosphate-41
1 mMWW3-5[U-100% 15N]2
2 mMHECT_PY-62
150 mMsodium chloride-72
20 mMsodium phosphate-82
0.8 mMWW3-9[U-100% 13C; U-100% 15N]3
1.6 mMHECT_PY-103
150 mMsodium chloride-113
20 mMsodium phosphate-123
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 615 / NOE intraresidue total count: 0 / NOE long range total count: 229 / NOE medium range total count: 70 / NOE sequential total count: 164
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 2 Å / Maximum upper distance constraint violation: 6.5 Å / Representative conformer: 1

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