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- PDB-2lb2: Structure of the second domain of human Nedd4L in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 2lb2
TitleStructure of the second domain of human Nedd4L in complex with a phosphorylated pTPY motif derived from human Smad3
Components
  • E3 ubiquitin-protein ligase NEDD4-like
  • Mothers against decapentaplegic homolog 3
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / Nedd4L / SMAD / CDK / signal transduction / SIGNALING PROTEIN-TRANSCRIPTION 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 / negative regulation of sodium ion import across plasma membrane / paraxial mesoderm morphogenesis / transdifferentiation / positive regulation of caveolin-mediated endocytosis / sterol response element binding / SMAD4 MH2 Domain Mutants in Cancer ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / negative regulation of sodium ion import across plasma membrane / paraxial mesoderm morphogenesis / transdifferentiation / positive regulation of caveolin-mediated endocytosis / sterol response element binding / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / 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 / co-SMAD binding / regulation of potassium ion transmembrane transporter activity / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / bHLH transcription factor binding / negative regulation of potassium ion transmembrane transport / positive regulation of chondrocyte differentiation / FOXO-mediated transcription of cell cycle genes / DEAD/H-box RNA helicase binding / regulation of transforming growth factor beta receptor signaling pathway / pericardium development / negative regulation of osteoblast proliferation / trophoblast cell migration / : / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / nuclear glucocorticoid receptor binding / embryonic foregut morphogenesis / negative regulation of wound healing / regulation of membrane repolarization / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / regulation of sodium ion transmembrane transport / transforming growth factor beta receptor binding / regulation of membrane depolarization / Germ layer formation at gastrulation / primary miRNA processing / potassium channel inhibitor activity / receptor catabolic process / positive regulation of dendrite extension / Formation of definitive endoderm / SMAD protein signal transduction / embryonic pattern specification / endoderm development / Signaling by Activin / ventricular cardiac muscle cell action potential / activin receptor signaling pathway / Formation of axial mesoderm / cell-cell junction organization / regulation of monoatomic ion transmembrane transport / Signaling by NODAL / HECT-type E3 ubiquitin transferase / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / I-SMAD binding / Interleukin-37 signaling / TGFBR3 expression / sodium channel inhibitor activity / response to angiotensin / nuclear inner membrane / signal transduction involved in regulation of gene expression / positive regulation of positive chemotaxis / osteoblast development / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of ossification / RUNX3 regulates CDKN1A transcription / ureteric bud development / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cytosolic calcium ion concentration / DNA-binding transcription repressor activity / adrenal gland development / regulation of dendrite morphogenesis / neuromuscular junction development / negative regulation of fat cell differentiation / regulation of synapse organization / heart looping / R-SMAD binding / TGF-beta receptor signaling activates SMADs / thyroid gland development / mesoderm formation / positive regulation of SMAD protein signal transduction / negative regulation of cell differentiation / sodium channel regulator activity / positive regulation of focal adhesion assembly / anatomical structure morphogenesis / protein monoubiquitination / negative regulation of osteoblast differentiation / developmental growth / regulation of immune response / positive regulation of bone mineralization
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 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 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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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)5,5262
Polymers5,5262
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)25 / 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: 4184.675 Da / Num. of mol.: 1 / Fragment: residues 386-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Production host: Escherichia coli (E. coli)
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: 1341.272 Da / Num. of mol.: 1 / Fragment: residues 178-189 / 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: Structure of the second domain of human Nedd4L in complex with a doubly phosphorylated human Smad3 (res 178-189) derived peptide.
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
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 766 / NOE intraresidue total count: 0 / NOE long range total count: 298 / NOE medium range total count: 47 / NOE sequential total count: 249 / Hydrogen bond constraints total count: 10
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 300 / Conformers submitted total number: 25

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