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- PDB-2ltz: Smurf2 WW3 domain in complex with a Smad7 derived peptide -

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Basic information

Entry
Database: PDB / ID: 2ltz
TitleSmurf2 WW3 domain in complex with a Smad7 derived peptide
Components
  • E3 ubiquitin-protein ligase SMURF2
  • Smad7 derived peptide
KeywordsPROTEIN BINDING/PEPTIDE / WW / SMURF2 / SMAD7 / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


positive regulation of chondrocyte hypertrophy / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / negative regulation of T cell cytokine production / heteromeric SMAD protein complex / regulation of ventricular cardiac muscle cell membrane depolarization / response to laminar fluid shear stress / negative regulation of T-helper 17 cell differentiation / positive regulation of cell-cell adhesion / positive regulation of trophoblast cell migration ...positive regulation of chondrocyte hypertrophy / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / negative regulation of T cell cytokine production / heteromeric SMAD protein complex / regulation of ventricular cardiac muscle cell membrane depolarization / response to laminar fluid shear stress / negative regulation of T-helper 17 cell differentiation / positive regulation of cell-cell adhesion / positive regulation of trophoblast cell migration / regulation of epithelial to mesenchymal transition / regulation of transforming growth factor beta receptor signaling pathway / activin receptor binding / negative regulation of epithelial to mesenchymal transition / negative regulation of transcription by competitive promoter binding / negative regulation of ubiquitin-protein transferase activity / Signaling by BMP / type I transforming growth factor beta receptor binding / HECT-type E3 ubiquitin transferase / negative regulation of activin receptor signaling pathway / SMAD protein signal transduction / protein-containing complex localization / adherens junction assembly / negative regulation of ossification / I-SMAD binding / transcription regulator inhibitor activity / Wnt signaling pathway, planar cell polarity pathway / ureteric bud development / artery morphogenesis / ventricular cardiac muscle tissue morphogenesis / ventricular septum morphogenesis / negative regulation of SMAD protein signal transduction / negative regulation of peptidyl-threonine phosphorylation / SMAD binding / ubiquitin-like ligase-substrate adaptor activity / negative regulation of BMP signaling pathway / anatomical structure morphogenesis / regulation of cardiac muscle contraction / ubiquitin ligase complex / negative regulation of peptidyl-serine phosphorylation / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / collagen binding / cellular response to leukemia inhibitory factor / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / Asymmetric localization of PCP proteins / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of transforming growth factor beta receptor signaling pathway / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / fibrillar center / beta-catenin binding / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / UCH proteinases / ubiquitin protein ligase activity / Interferon gamma signaling / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein stabilization / protein ubiquitination / Ub-specific processing proteases / nuclear speck / membrane raft / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / SMAD/FHA domain superfamily / 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 SMURF2
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 SMURF2
B: Smad7 derived peptide


Theoretical massNumber of molelcules
Total (without water)5,9842
Polymers5,9842
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

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


Mass: 4204.599 Da / Num. of mol.: 1 / Fragment: WW3 domain (UNP residues 297-333)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF2 / Plasmid: petM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HAU4
#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 SMURF2WW3, 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] SMURF2WW3, 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 mMSMURF2WW3-11
2 mMSMAD7-21
20 mMTRIS-3[U-100% 2H]1
100 mMsodium chloride-41
1 mMSMURF2WW3-5[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: 20

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