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- PDB-2lay: Structure of the first WW domain of human YAP in complex with a p... -

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Basic information

Entry
Database: PDB / ID: 2lay
TitleStructure of the first WW domain of human YAP in complex with a phosphorylated human Smad1 derived peptide
Components
  • Mothers against decapentaplegic homolog 1
  • Yorkie homolog
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / YAP / SMAD / CDK / signal transduction / SIGNALING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


mesodermal cell fate commitment / homomeric SMAD protein complex / osteoblast fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / SMAD protein complex / RUNX2 regulates bone development / co-SMAD binding / heteromeric SMAD protein complex / regulation of metanephric nephron tubule epithelial cell differentiation ...mesodermal cell fate commitment / homomeric SMAD protein complex / osteoblast fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / SMAD protein complex / RUNX2 regulates bone development / co-SMAD binding / heteromeric SMAD protein complex / regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation of muscle cell differentiation / cardiac muscle tissue regeneration / positive regulation of cartilage development / glandular epithelial cell differentiation / TEAD-YAP complex / primary miRNA binding / DEAD/H-box RNA helicase binding / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / gamete generation / hindbrain development / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / primary miRNA processing / paraxial mesoderm development / regulation of stem cell proliferation / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Signaling by BMP / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / embryonic pattern specification / SMAD protein signal transduction / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / I-SMAD binding / proline-rich region binding / Signaling by Hippo / cartilage development / Cardiogenesis / nuclear inner membrane / cardiac muscle cell proliferation / ureteric bud development / negative regulation of epithelial cell differentiation / midbrain development / organ growth / homeostatic process / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of sprouting angiogenesis / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / cellular response to organic cyclic compound / regulation of neurogenesis / anatomical structure morphogenesis / canonical Wnt signaling pathway / vasculogenesis / BMP signaling pathway / 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 / ossification / transforming growth factor beta receptor signaling pathway / epithelial cell proliferation / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / wound healing / bone development / cell morphogenesis / cellular response to gamma radiation / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / transcription corepressor activity / MAPK cascade / cell-cell junction / positive regulation of canonical Wnt signaling pathway / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription by RNA polymerase II
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
Transcriptional coactivator YAP1 / Mothers against decapentaplegic homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMacias, M.J. / Aragon, E. / Goerner, N. / Zaromytidou, A. / Xi, Q. / Escobedo, A. / Massague, J.
CitationJournal: Genes Dev. / Year: 2011
Title: A Smad action turnover switch operated by WW domain readers of a phosphoserine code.
Authors: Aragon, E. / Goerner, N. / Zaromytidou, A.I. / Xi, Q. / Escobedo, A. / Massague, J. / Macias, M.J.
History
DepositionMar 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Yorkie homolog
B: Mothers against decapentaplegic homolog 1


Theoretical massNumber of molelcules
Total (without water)5,2092
Polymers5,2092
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)20 / 300structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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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: residues 170-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YAP1, YAP65 / Production host: Escherichia coli (E. coli) / References: UniProt: P46937
#2: Protein/peptide Mothers against decapentaplegic homolog 1 / MAD homolog 1 / Mothers against DPP homolog 1 / JV4-1 / Mad-related protein 1 / SMAD family member ...MAD homolog 1 / Mothers against DPP homolog 1 / JV4-1 / Mad-related protein 1 / SMAD family member 1 / SMAD 1 / Smad1 / hSMAD1 / Transforming growth factor-beta-signaling protein 1 / BSP-1


Mass: 1056.985 Da / Num. of mol.: 1 / Fragment: residues 201-209 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15797

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the first domain of human Yap in complex with a human Smad1 derived peptide.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1333D CBCA(CO)NH
1433D HN(CA)CB
1522D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNEDD4LWW3-11
3 mMSMAD3-21
20 mMsodium phosphate-31
100 mMsodium chloride-41
2 mMsodium azide-51
1 mMNEDD4LWW3-6[U-100% 15N]2
3 mMSMAD3-72
20 mMsodium phosphate-82
100 mMsodium chloride-92
2 mMsodium azide-102
1 mMNEDD4LWW3-11[U-100% 13C; U-100% 15N]3
3 mMSMAD3-123
20 mMsodium phosphate-133
100 mMsodium chloride-143
2 mMsodium azide-153
Sample conditionsIonic strength: 0.420 / pH: 7 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
XEASYBartels et al.chemical shift assignment
TOPSPINBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 625 / NOE intraresidue total count: 0 / NOE long range total count: 258 / NOE medium range total count: 81 / NOE sequential total count: 172 / Hydrogen bond constraints total count: 10
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 300 / Conformers submitted total number: 20

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