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- PDB-2ltx: Smurf1 WW2 domain in complex with a Smad7 derived peptide -

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Basic information

Entry
Database: PDB / ID: 2ltx
TitleSmurf1 WW2 domain in complex with a Smad7 derived peptide
Components
  • E3 ubiquitin-protein ligase SMURF1
  • Smad7 derived peptide
KeywordsPROTEIN BINDING/PEPTIDE / WW / SMURF1 / SMAD7 / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


positive regulation of chondrocyte hypertrophy / beta-catenin destruction complex disassembly / substrate localization to autophagosome / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / engulfment of target by autophagosome / negative regulation of T cell cytokine production / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex / protein targeting to vacuole involved in autophagy ...positive regulation of chondrocyte hypertrophy / beta-catenin destruction complex disassembly / substrate localization to autophagosome / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / engulfment of target by autophagosome / negative regulation of T cell cytokine production / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex / protein targeting to vacuole involved in autophagy / regulation of ventricular cardiac muscle cell membrane depolarization / negative regulation of T-helper 17 cell differentiation / protein-containing complex disassembly / activin receptor binding / response to laminar fluid shear stress / ectoderm development / transforming growth factor beta receptor binding / receptor catabolic process / negative regulation of transcription by competitive promoter binding / regulation of epithelial to mesenchymal transition / 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 / protein-containing complex localization / HECT-type E3 ubiquitin transferase / adherens junction assembly / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / 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 / R-SMAD binding / negative regulation of BMP signaling pathway / anatomical structure morphogenesis / regulation of cardiac muscle contraction / positive regulation of axon extension / BMP signaling pathway / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / collagen binding / transforming growth factor beta receptor signaling pathway / protein export from nucleus / cellular response to leukemia inhibitory factor / negative regulation of cell migration / Downregulation of TGF-beta receptor signaling / protein localization to plasma membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Asymmetric localization of PCP proteins / 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 / phospholipid binding / fibrillar center / protein polyubiquitination / Interferon gamma signaling / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein stabilization / Ub-specific processing proteases / ciliary basal body / axon / neuronal cell body / centrosome / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / metal ion 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 / 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 SMURF1
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SMURF1
B: Smad7 derived peptide


Theoretical massNumber of molelcules
Total (without water)5,8362
Polymers5,8362
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 the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase SMURF1 / hSMURF1 / SMAD ubiquitination regulatory factor 1 / SMAD-specific E3 ubiquitin-protein ligase 1


Mass: 4057.490 Da / Num. of mol.: 1 / Fragment: WW2 domain (UNP residues 306-340)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF1, KIAA1625 / Plasmid: petM11 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 / References: UniProt: Q9HCE7
#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 SMURF1WW2, 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] SMURF1WW2, 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 mMSMURF1WW2-11
2 mMSMAD7-21
20 mMTRIS-3[U-100% 2H]1
100 mMsodium chloride-41
1 mMSMURF1WW2-5[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: 25

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