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- PDB-2ltv: YAP WW2 in complex with a Smad7 derived peptide -

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Basic information

Entry
Database: PDB / ID: 2ltv
TitleYAP WW2 in complex with a Smad7 derived peptide
Components
  • Smad7 derived peptide
  • Yorkie homolog
KeywordsPROTEIN BINDING/PEPTIDE / WW / YAP / 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 / enterocyte differentiation / regulation of keratinocyte proliferation / heteromeric SMAD protein complex / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / regulation of ventricular cardiac muscle cell membrane depolarization ...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 / enterocyte differentiation / regulation of keratinocyte proliferation / heteromeric SMAD protein complex / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / regulation of ventricular cardiac muscle cell membrane depolarization / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / positive regulation of cell-cell adhesion / negative regulation of T-helper 17 cell differentiation / response to laminar fluid shear stress / notochord development / negative regulation of cilium assembly / regulation of epithelial to mesenchymal transition / activin receptor binding / lung epithelial cell differentiation / regulation of transforming growth factor beta receptor signaling pathway / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / regulation of stem cell proliferation / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / 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 / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / adherens junction assembly / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / Formation of axial mesoderm / negative regulation of stem cell differentiation / protein-containing complex localization / embryonic heart tube morphogenesis / negative regulation of epithelial to mesenchymal transition / female germ cell nucleus / I-SMAD binding / negative regulation of ossification / proline-rich region binding / transcription regulator inhibitor activity / Signaling by Hippo / ventricular cardiac muscle tissue morphogenesis / artery morphogenesis / ureteric bud development / negative regulation of epithelial cell differentiation / organ growth / ventricular septum morphogenesis / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / negative regulation of SMAD protein signal transduction / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / RUNX2 regulates osteoblast differentiation / negative regulation of peptidyl-serine phosphorylation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / ubiquitin-like ligase-substrate adaptor activity / negative regulation of BMP signaling pathway / regulation of neurogenesis / regulation of cardiac muscle contraction / anatomical structure morphogenesis / canonical Wnt signaling pathway / vasculogenesis / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / collagen binding / negative regulation of cell migration / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / epithelial cell proliferation / cellular response to leukemia inhibitory factor / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / fibrillar center
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 / SMAD-like domain superfamily / SMAD/FHA domain superfamily / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 7 / Transcriptional coactivator YAP1
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: Yorkie homolog
B: Smad7 derived peptide


Theoretical massNumber of molelcules
Total (without water)5,5992
Polymers5,5992
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)40 / 300structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Yorkie homolog / 65 kDa Yes-associated protein / YAP65


Mass: 4191.591 Da / Num. of mol.: 1 / Fragment: WW2 domain (UNP residues 230-265)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YAP1, YAP65 / Plasmid: petM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P46937
#2: Protein/peptide Smad7 derived peptide


Mass: 1407.570 Da / Num. of mol.: 1 / Fragment: UNP residues 206-217 / 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 YAPWW2, 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] YAPWW2, 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 mMYAPWW2-11
2 mMSMAD7-21
20 mMTRIS-3[U-100% 2H]1
100 mMsodium chloride-41
1 mMYAPWW2-5[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: 40

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