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- PDB-5ydy: NMR structure of YAP1-2 WW2 domain with LATS1 PPxY motif complex -

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Basic information

Entry
Database: PDB / ID: 5ydy
TitleNMR structure of YAP1-2 WW2 domain with LATS1 PPxY motif complex
ComponentsWW2 domain and PPxY motif complex
KeywordsSIGNALING PROTEIN / Hippo pathway / YAP / LATs / WW domain / PPxY motif
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / 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 ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / 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 / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / 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 / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / negative regulation of epithelial cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / 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 / epithelial cell proliferation / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / 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 factor binding / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA damage response / chromatin binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFan, J.S. / Sivaraman, J.
CitationJournal: Oncotarget / Year: 2018
Title: Biophysical studies and NMR structure of YAP2 WW domain - LATS1 PPxY motif complexes reveal the basis of their interaction.
Authors: Verma, A. / Jing-Song, F. / Finch-Edmondson, M.L. / Velazquez-Campoy, A. / Balasegaran, S. / Sudol, M. / Sivaraman, J.
History
DepositionSep 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
Revision 1.2May 22, 2019Group: Data collection / Refinement description / Category: refine
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WW2 domain and PPxY motif complex


Theoretical massNumber of molelcules
Total (without water)5,9981
Polymers5,9981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4650 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein WW2 domain and PPxY motif complex


Mass: 5997.581 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WW2 domain and PPxY motif complex / Source: (gene. exp.) Homo sapiens (human) / Production host: Cloning vector pGEM3_Zf (others) / References: UniProt: P46937*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic12D 1H-1H NOESY
121isotropic13D 1H-15N TOCSY
131isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-100% 15N] WW2 domain and PPxY motif complex, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21.00 mM WW2 domain and PPxY motif complex, 100% D2Oun-labelled100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMWW2 domain and PPxY motif complex[U-100% 15N]1
1.00 mMWW2 domain and PPxY motif complexnatural abundance2
Sample conditions

Ionic strength: 100 mM / Ionic strength err: 0.2 / pH: 6.0 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

Conditions-IDLabel
1H2O
2D2O

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.22data extraction
NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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