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- PDB-2lty: NEDD4L WW2 domain in complex with a Smad7 derived peptide -

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Basic information

Entry
Database: PDB / ID: 2lty
TitleNEDD4L WW2 domain in complex with a Smad7 derived peptide
Components
  • E3 ubiquitin-protein ligase NEDD4-like
  • Smad7 derived peptide
KeywordsPROTEIN BINDING/PEPTIDE / WW / NEDD4L / SMAD7 / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


positive regulation of chondrocyte hypertrophy / beta-catenin destruction complex disassembly / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / negative regulation of sodium ion import across plasma membrane / positive regulation of caveolin-mediated endocytosis / negative regulation of T cell cytokine production / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / positive regulation of cell-cell adhesion mediated by cadherin ...positive regulation of chondrocyte hypertrophy / beta-catenin destruction complex disassembly / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / negative regulation of sodium ion import across plasma membrane / positive regulation of caveolin-mediated endocytosis / negative regulation of T cell cytokine production / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex / regulation of potassium ion transmembrane transporter activity / regulation of ventricular cardiac muscle cell membrane depolarization / negative regulation of T-helper 17 cell differentiation / negative regulation of potassium ion transmembrane transport / protein-containing complex disassembly / : / activin receptor binding / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / response to laminar fluid shear stress / regulation of membrane repolarization / regulation of sodium ion transmembrane transport / regulation of membrane depolarization / potassium channel inhibitor activity / receptor catabolic process / regulation of epithelial to mesenchymal transition / negative regulation of transcription by competitive promoter binding / positive regulation of dendrite extension / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / Signaling by BMP / negative regulation of activin receptor signaling pathway / ventricular cardiac muscle cell action potential / protein-containing complex localization / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / adherens junction assembly / I-SMAD binding / sodium channel inhibitor activity / negative regulation of ossification / artery morphogenesis / ureteric bud development / negative regulation of epithelial to mesenchymal transition / regulation of dendrite morphogenesis / ventricular cardiac muscle tissue morphogenesis / neuromuscular junction development / ventricular septum morphogenesis / negative regulation of SMAD protein signal transduction / regulation of synapse organization / negative regulation of BMP signaling pathway / sodium channel regulator activity / protein monoubiquitination / anatomical structure morphogenesis / regulation of cardiac muscle contraction / ubiquitin-like ligase-substrate adaptor activity / potassium channel regulator activity / protein K48-linked ubiquitination / transcription regulator inhibitor activity / collagen binding / multivesicular body / transforming growth factor beta receptor signaling pathway / cellular response to leukemia inhibitory factor / negative regulation of cell migration / Downregulation of TGF-beta receptor signaling / regulation of membrane potential / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Budding and maturation of HIV virion / regulation of protein stability / beta-catenin binding / receptor internalization / Stimuli-sensing channels / fibrillar center / positive regulation of protein catabolic process / Interferon gamma signaling / neuron projection development / ubiquitin-protein transferase activity / transcription corepressor activity / UCH proteinases / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / monoatomic ion transmembrane transport / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / cell differentiation / protein stabilization / Ub-specific processing proteases / protein ubiquitination / ciliary basal body / apical plasma membrane / centrosome / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / Golgi apparatus
Similarity search - Function
MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain ...MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / E3 ubiquitin-protein ligase, SMURF1 type / SMAD-like domain superfamily / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / SMAD/FHA domain superfamily / 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
Mothers against decapentaplegic homolog 7 / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMacias, M.J. / Aragon, E. / Goerner, N. / Xi, Q. / Lopes, T. / Gao, S. / Massague, J.
CitationJournal: Structure / Year: 2012
Title: Structural Basis for the Versatile Interactions of Smad7 with Regulator WW Domains in TGF-beta Pathways.
Authors: Aragon, E. / Goerner, N. / Xi, Q. / Gomes, T. / Gao, S. / Massague, J. / Macias, M.J.
History
DepositionJun 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_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: Smad7 derived peptide


Theoretical massNumber of molelcules
Total (without water)5,7452
Polymers5,7452
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)30 / 300structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

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


Mass: 3966.360 Da / Num. of mol.: 1 / Fragment: WW2 domain (UNP residues 385-417)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Plasmid: petM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q96PU5
#2: Protein/peptide Smad7 derived peptide


Mass: 1778.955 Da / Num. of mol.: 1 / Fragment: UNP residues 203-217 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15105

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1423D CBCA(CO)NH
1523D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM NEDD4LWW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] NEDD4LWW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNEDD4LWW2-11
2 mMSMAD7-21
20 mMTRIS-3[U-100% 2H]1
100 mMsodium chloride-41
1 mMNEDD4LWW2-5[U-100% 13C; U-100% 15N]2
3 mMSMAD7-62
20 mMTRIS-7[U-100% 2H]2
100 mMsodium chloride-82
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 285 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
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 30

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