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- PDB-2laj: Third WW domain of human Nedd4L in complex with doubly phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 2laj
TitleThird WW domain of human Nedd4L in complex with doubly phosphorylated human smad3 derived peptide
Components
  • E3 ubiquitin-protein ligase NEDD4-like
  • Mothers against decapentaplegic homolog 3
KeywordsLIGASE/TRANSCRIPTION REGULATOR / CDK / signal transduction / LIGASE-TRANSCRIPTION REGULATOR complex
Function / homology
Function and homology information


nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / sterol response element binding / transdifferentiation / paraxial mesoderm morphogenesis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / positive regulation of caveolin-mediated endocytosis ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / sterol response element binding / transdifferentiation / paraxial mesoderm morphogenesis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / positive regulation of caveolin-mediated endocytosis / nodal signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / SMAD protein complex / immune system development / regulation of striated muscle tissue development / heteromeric SMAD protein complex / pericardium development / co-SMAD binding / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / bHLH transcription factor binding / negative regulation of sodium ion import across plasma membrane / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport / DEAD/H-box RNA helicase binding / FOXO-mediated transcription of cell cycle genes / regulation of transforming growth factor beta receptor signaling pathway / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / trophoblast cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of protein localization to cell surface / positive regulation of extracellular matrix assembly / negative regulation of wound healing / embryonic foregut morphogenesis / nuclear glucocorticoid receptor binding / positive regulation of dendrite extension / lens fiber cell differentiation / regulation of membrane repolarization / regulation of membrane depolarization / Germ layer formation at gastrulation / primary miRNA processing / transforming growth factor beta receptor binding / receptor catabolic process / regulation of sodium ion transmembrane transport / SMAD protein signal transduction / Formation of definitive endoderm / embryonic pattern specification / potassium channel inhibitor activity / endoderm development / Signaling by Activin / embryonic cranial skeleton morphogenesis / activin receptor signaling pathway / ventricular cardiac muscle cell action potential / Formation of axial mesoderm / response to angiotensin / Signaling by NODAL / regulation of epithelial cell proliferation / HECT-type E3 ubiquitin transferase / Interleukin-37 signaling / cell-cell junction organization / sodium channel inhibitor activity / I-SMAD binding / TGFBR3 expression / nuclear inner membrane / positive regulation of positive chemotaxis / negative regulation of ossification / NOTCH4 Intracellular Domain Regulates Transcription / RUNX3 regulates CDKN1A transcription / osteoblast development / signal transduction involved in regulation of gene expression / ureteric bud development / DNA-binding transcription repressor activity / adrenal gland development / negative regulation of cardiac muscle hypertrophy in response to stress / regulation of dendrite morphogenesis / negative regulation of cytosolic calcium ion concentration / negative regulation of fat cell differentiation / neuromuscular junction development / heart looping / regulation of synapse organization / TGF-beta receptor signaling activates SMADs / thyroid gland development / R-SMAD binding / mesoderm formation / positive regulation of SMAD protein signal transduction / negative regulation of cell differentiation / developmental growth / positive regulation of focal adhesion assembly / sodium channel regulator activity / anatomical structure morphogenesis / protein monoubiquitination / regulation of immune response / negative regulation of osteoblast differentiation / positive regulation of bone mineralization / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / phosphatase binding / somitogenesis
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 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / E3 ubiquitin-protein ligase, SMURF1 type / SMAD-like domain superfamily / 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 / SMAD/FHA domain superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / C2 domain / C2 domain profile. / WW/rsp5/WWP domain signature. / 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
Mothers against decapentaplegic homolog 3 / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMacias, M.J. / Aragon, E. / Goerner, N. / Zaromytidou, A. / Xi, Q. / Escobedo, A. / Massague, J.
CitationJournal: Genes Dev. / Year: 2011
Title: A Smad action turnover switch operated by WW domain readers of a phosphoserine code.
Authors: Aragon, E. / Goerner, N. / Zaromytidou, A.I. / Xi, Q. / Escobedo, A. / Massague, J. / Macias, M.J.
History
DepositionMar 16, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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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: Mothers against decapentaplegic homolog 3


Theoretical massNumber of molelcules
Total (without water)6,3242
Polymers6,3242
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)15 / 300structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

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


Mass: 5210.877 Da / Num. of mol.: 1 / Fragment: WW 3 domain residues 496-535
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
References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Mothers against decapentaplegic homolog 3 / MAD homolog 3 / Mad3 / Mothers against DPP homolog 3 / hMAD-3 / JV15-2 / SMAD family member 3 / ...MAD homolog 3 / Mad3 / Mothers against DPP homolog 3 / hMAD-3 / JV15-2 / SMAD family member 3 / SMAD 3 / Smad3 / hSMAD3


Mass: 1112.966 Da / Num. of mol.: 1 / Fragment: sequence database residues 202-211 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84022
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Third WW domain of human Nedd4L (residues 476-515) in complex with doubly phosphorylated human smad3 derived peptide (residues 202-211).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1333D CBCA(CO)NH
1433D HN(CA)CB
1522D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNEDD4LWW3-11
3 mMSMAD3-21
20 mMsodium phosphate-31
100 mMsodium chloride-41
2 mMsodium azide-51
1 mMNEDD4LWW3-6[U-100% 15N]2
3 mMSMAD3-72
20 mMsodium phosphate-82
100 mMsodium chloride-92
2 mMsodium azide-102
1 mMNEDD4LWW3-11[U-100% 13C; U-100% 15N]3
3 mMSMAD3-123
20 mMsodium phosphate-133
100 mMsodium chloride-143
2 mMsodium azide-153
Sample conditionsIonic strength: 0.42 / pH: 7 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 448 / NOE intraresidue total count: 0 / NOE long range total count: 237 / NOE medium range total count: 53 / NOE sequential total count: 174
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 300 / Conformers submitted total number: 15

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