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- PDB-2djy: Solution structure of Smurf2 WW3 domain-Smad7 PY peptide complex -

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Basic information

Entry
Database: PDB / ID: 2djy
TitleSolution structure of Smurf2 WW3 domain-Smad7 PY peptide complex
Components
  • Mothers against decapentaplegic homolog 7
  • Smad ubiquitination regulatory factor 2
KeywordsLIGASE/SIGNALING PROTEIN / beta sheet / polyproline type II helix / PPII / LIGASE-SIGNALING PROTEIN 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 T cell cytokine production / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex / regulation of ventricular cardiac muscle cell membrane depolarization / negative regulation of T-helper 17 cell differentiation / regulation of transforming growth factor beta receptor signaling pathway ...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 T cell cytokine production / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex / regulation of ventricular cardiac muscle cell membrane depolarization / negative regulation of T-helper 17 cell differentiation / regulation of transforming growth factor beta receptor signaling pathway / protein-containing complex disassembly / positive regulation of trophoblast cell migration / activin receptor binding / response to laminar fluid shear stress / negative regulation of transcription by competitive promoter binding / regulation of epithelial to mesenchymal transition / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / Signaling by BMP / negative regulation of activin receptor signaling pathway / protein-containing complex localization / HECT-type E3 ubiquitin transferase / adherens junction assembly / I-SMAD binding / negative regulation of ossification / Wnt signaling pathway, planar cell polarity pathway / artery morphogenesis / ureteric bud development / negative regulation of epithelial to mesenchymal transition / ventricular cardiac muscle tissue morphogenesis / ventricular septum morphogenesis / negative regulation of SMAD protein signal transduction / SMAD binding / negative regulation of BMP signaling pathway / anatomical structure morphogenesis / ubiquitin ligase complex / regulation of cardiac muscle contraction / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / collagen binding / transforming growth factor beta receptor signaling pathway / cellular response to leukemia inhibitory factor / negative regulation of cell migration / Downregulation of TGF-beta receptor signaling / Asymmetric localization of PCP proteins / Degradation of AXIN / negative regulation of transforming growth factor beta receptor signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / beta-catenin binding / fibrillar center / Interferon gamma signaling / ubiquitin-protein transferase activity / transcription corepressor activity / UCH proteinases / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein stabilization / Ub-specific processing proteases / nuclear speck / protein ubiquitination / ciliary basal body / membrane raft / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / 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 / Single Sheet / C2 domain superfamily / Mainly Beta
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 7 / E3 ubiquitin-protein ligase SMURF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsChong, P.A. / Lin, H / Wrana, J.L. / Forman-Kay, J.D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: An Expanded WW Domain Recognition Motif Revealed by the Interaction between Smad7 and the E3 Ubiquitin Ligase Smurf2.
Authors: Chong, P.A. / Lin, H. / Wrana, J.L. / Forman-Kay, J.D.
History
DepositionApr 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Smad ubiquitination regulatory factor 2
B: Mothers against decapentaplegic homolog 7


Theoretical massNumber of molelcules
Total (without water)6,8062
Polymers6,8062
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Smad ubiquitination regulatory factor 2 / Ubiquitin--protein ligase SMURF2 / Smad-specific E3 ubiquitin ligase 2 / hSMURF2


Mass: 4616.053 Da / Num. of mol.: 1 / Fragment: WW3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF2 / Plasmid: pGEX6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: Q9HAU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Mothers against decapentaplegic homolog 7 / SMAD 7 / Mothers against DPP homolog 7 / Smad7 / hSMAD7


Mass: 2190.409 Da / Num. of mol.: 1 / Fragment: PY motif region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD7, MADH7, MADH8 / Plasmid: pGEX6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O15105

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionClassification
NMRPipe2.3processing
ARIA1.2refinement
NMRView5.2.2data analysis
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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