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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 / response to laminar fluid shear stress / negative regulation of T cell cytokine production / regulation of ventricular cardiac muscle cell membrane depolarization / regulation of stem cell proliferation / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex ...positive regulation of chondrocyte hypertrophy / beta-catenin destruction complex disassembly / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / response to laminar fluid shear stress / negative regulation of T cell cytokine production / regulation of ventricular cardiac muscle cell membrane depolarization / regulation of stem cell proliferation / positive regulation of cell-cell adhesion mediated by cadherin / heteromeric SMAD protein complex / cardiac muscle tissue regeneration / polarized epithelial cell differentiation / TEAD-YAP complex / negative regulation of T-helper 17 cell differentiation / negative regulation of epithelial cell apoptotic process / protein-containing complex disassembly / RUNX3 regulates YAP1-mediated transcription / organ growth / negative regulation of cilium assembly / tissue homeostasis / epithelial cell proliferation / activin receptor binding / regulation of epithelial to mesenchymal transition / YAP1- and WWTR1 (TAZ)-stimulated gene expression / SMAD protein signal transduction / intestinal epithelial cell development / : / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Signaling by BMP / protein-containing complex localization / negative regulation of ossification / type I transforming growth factor beta receptor binding / Formation of axial mesoderm / ureteric bud development / negative regulation of activin receptor signaling pathway / artery morphogenesis / heart process / Signaling by Hippo / proline-rich region binding / I-SMAD binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / adherens junction assembly / negative regulation of fat cell differentiation / ventricular septum morphogenesis / negative regulation of epithelial to mesenchymal transition / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / ventricular cardiac muscle tissue morphogenesis / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / negative regulation of SMAD protein signal transduction / positive regulation of cardiac muscle cell proliferation / positive regulation of osteoblast differentiation / response to progesterone / negative regulation of BMP signaling pathway / regulation of neurogenesis / bicellular tight junction / transforming growth factor beta receptor signaling pathway / anatomical structure morphogenesis / Nuclear signaling by ERBB4 / regulation of cardiac muscle contraction / transcription regulator inhibitor activity / ubiquitin-like ligase-substrate adaptor activity / collagen binding / positive regulation of epithelial cell proliferation / negative regulation of cell migration / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / Developmental Lineage of Pancreatic Ductal Cells / Downregulation of TGF-beta receptor signaling / cellular response to gamma radiation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of protein localization to nucleus / fibrillar center / beta-catenin binding / Interferon gamma signaling / transcription coregulator activity / cell-cell junction / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PD-L1(CD274) transcription / UCH proteinases / positive regulation of cell growth / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ciliary basal body / protein-containing complex assembly / DNA-binding transcription factor binding / cell differentiation / transcription coactivator activity / protein stabilization / transcription cis-regulatory region binding / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin binding
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
SMAD family member 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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