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- PDB-2ltw: YAP WW1 in complex with a Smad7 derived peptide -

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Basic information

Entry
Database: PDB / ID: 2ltw
TitleYAP WW1 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 / 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 / enterocyte differentiation / regulation of keratinocyte proliferation / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex / regulation of metanephric nephron tubule epithelial cell differentiation ...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 / enterocyte differentiation / regulation of keratinocyte proliferation / positive regulation of cell-cell adhesion mediated by cadherin / 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 / negative regulation of T-helper 17 cell differentiation / TEAD-YAP complex / lateral mesoderm development / polarized epithelial cell differentiation / bud elongation involved in lung branching / protein-containing complex disassembly / RUNX3 regulates YAP1-mediated transcription / notochord development / activin receptor binding / negative regulation of cilium assembly / lung epithelial cell differentiation / response to laminar fluid shear stress / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of epithelial to mesenchymal transition / regulation of stem cell proliferation / negative regulation of transcription by competitive promoter binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of epithelial cell apoptotic process / intestinal epithelial cell development / tissue homeostasis / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / Signaling by BMP / negative regulation of activin receptor signaling pathway / Formation of axial mesoderm / protein-containing complex localization / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / adherens junction assembly / I-SMAD binding / proline-rich region binding / Signaling by Hippo / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / negative regulation of ossification / artery morphogenesis / ureteric bud development / negative regulation of epithelial to mesenchymal transition / organ growth / negative regulation of epithelial cell differentiation / ventricular cardiac muscle tissue morphogenesis / interleukin-6-mediated signaling pathway / ventricular septum morphogenesis / negative regulation of SMAD protein signal transduction / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / RUNX2 regulates osteoblast differentiation / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / regulation of neurogenesis / somatic stem cell population maintenance / negative regulation of BMP signaling pathway / anatomical structure morphogenesis / bicellular tight junction / regulation of cardiac muscle contraction / canonical Wnt signaling pathway / ubiquitin-like ligase-substrate adaptor activity / positive regulation of osteoblast differentiation / vasculogenesis / transcription regulator inhibitor activity / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / cellular response to retinoic acid / collagen binding / extrinsic apoptotic signaling pathway / transforming growth factor beta receptor signaling pathway / cellular response to leukemia inhibitory factor / negative regulation of cell migration / Downregulation of TGF-beta receptor signaling / response to progesterone / positive regulation of epithelial cell proliferation / epithelial cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to gamma radiation / cell morphogenesis / beta-catenin binding
Similarity search - Function
: / Omega loop, TEAD interating region 3 / : / 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. ...: / Omega loop, TEAD interating region 3 / : / 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)5,7452
Polymers5,7452
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 / 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: 4151.594 Da / Num. of mol.: 1 / Fragment: WW1 domain (UNP residues 170-205)
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: 1593.735 Da / Num. of mol.: 1 / Fragment: UNP residues 205-217 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15105
Sequence detailsTHIS IS A SMAD7 DERIVED PEPTIDE.

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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 YAPWW1, 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] YAPWW1, 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 mMYAPWW1-11
2 mMSMAD7-21
20 mMTRIS-3[U-100% 2H]1
100 mMsodium chloride-41
1 mMYAPWW1-5[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: 30

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