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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 / beta-catenin destruction complex disassembly / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / enterocyte differentiation / response to laminar fluid shear stress / negative regulation of T cell cytokine production / regulation of keratinocyte proliferation / regulation of ventricular cardiac muscle cell membrane depolarization / positive regulation of cell-cell adhesion mediated by cadherin ...positive regulation of chondrocyte hypertrophy / beta-catenin destruction complex disassembly / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / enterocyte differentiation / response to laminar fluid shear stress / negative regulation of T cell cytokine production / regulation of keratinocyte proliferation / regulation of ventricular cardiac muscle cell membrane depolarization / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex / glandular epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / negative regulation of T-helper 17 cell differentiation / lateral mesoderm development / bud elongation involved in lung branching / polarized epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription / notochord development / negative regulation of cilium assembly / activin receptor binding / protein-containing complex disassembly / lung epithelial cell differentiation / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / regulation of epithelial to mesenchymal transition / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of stem cell proliferation / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of transcription by competitive promoter binding / SMAD protein signal transduction / Signaling by BMP / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / protein-containing complex localization / female germ cell nucleus / I-SMAD binding / Signaling by Hippo / proline-rich region binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / adherens junction assembly / negative regulation of ossification / artery morphogenesis / ureteric bud development / negative regulation of epithelial to mesenchymal transition / organ growth / ventricular cardiac muscle tissue morphogenesis / negative regulation of epithelial cell differentiation / interleukin-6-mediated signaling pathway / ventricular septum morphogenesis / negative regulation of fat cell differentiation / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / negative regulation of SMAD protein signal transduction / Zygotic genome activation (ZGA) / positive regulation of stem cell population maintenance / somatic stem cell population maintenance / anatomical structure morphogenesis / negative regulation of BMP signaling pathway / regulation of neurogenesis / bicellular tight junction / regulation of cardiac muscle contraction / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / ubiquitin-like ligase-substrate adaptor activity / Nuclear signaling by ERBB4 / transcription regulator inhibitor activity / positive regulation of cardiac muscle cell proliferation / keratinocyte differentiation / collagen binding / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / transforming growth factor beta receptor signaling pathway / response to progesterone / negative regulation of cell migration / cellular response to leukemia inhibitory factor / Downregulation of TGF-beta receptor signaling / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / epithelial cell proliferation / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / wound healing / negative regulation of transforming growth factor beta receptor signaling pathway / cellular response to gamma radiation / beta-catenin binding / positive regulation of protein localization to nucleus
Similarity search - Function
: / Omega loop, TEAD interacting 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 interacting 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)5,5992
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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