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- PDB-8wrg: Solution structure of the TAD domain (450-504) of human transcrip... -

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Basic information

Entry
Database: PDB / ID: 8wrg
TitleSolution structure of the TAD domain (450-504) of human transcriptional coactivator YAP1
ComponentsTranscriptional coactivator YAP1
KeywordsTRANSCRIPTION / transcriptional coactivator / transcription factor complex
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 / polarized epithelial cell differentiation / bud elongation involved in lung branching / RUNX3 regulates YAP1-mediated transcription ...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 / polarized epithelial cell differentiation / bud elongation involved in lung branching / RUNX3 regulates YAP1-mediated transcription / 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 / hippo signaling / regulation of stem cell proliferation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of epithelial cell apoptotic process / intestinal epithelial cell development / tissue homeostasis / 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 / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / organ growth / negative regulation of epithelial cell differentiation / interleukin-6-mediated signaling pathway / 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 / bicellular tight junction / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / 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 / wound healing / cellular response to gamma radiation / cell morphogenesis / positive regulation of protein localization to nucleus / transcription corepressor activity / cell junction / positive regulation of canonical Wnt signaling pathway / cell-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 / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Omega loop, TEAD interating region 3 / : / 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
AuthorsZhang, H. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172299 China
CitationJournal: Nat Commun / Year: 2025
Title: The mechanism of YAP/TAZ transactivation and dual targeting for cancer therapy.
Authors: Yu, M. / Wang, J. / Zhang, X. / Zhang, H. / Li, C. / Li, J. / Lin, J. / Zheng, J. / Huang, L. / Li, Y. / Sun, S.
History
DepositionOct 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional coactivator YAP1


Theoretical massNumber of molelcules
Total (without water)7,0491
Polymers7,0491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional coactivator YAP1


Mass: 7048.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YAP1 / Variant: YAP1-2gamma / Production host: Escherichia coli (E. coli) / References: UniProt: P46937
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic13D CBCA(CO)NH
132isotropic13D CBCANH
142isotropic13D HNCO
152isotropic13D H(CCO)NH
162isotropic13D C(CO)NH
172isotropic13D HBHA(CO)NH
182isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 0.95 mM [U-99% 13C; U-99% 15N] YAP-TAD, 20 mM HEPES, 100 mM sodium chloride, 5 % v/v [U-99% 2H] D2O, 95% H2O/5% D2O
Label: 13C15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.95 mMYAP-TAD[U-99% 13C; U-99% 15N]2
20 mMHEPESnatural abundance2
100 mMsodium chloridenatural abundance2
5 % v/vD2O[U-99% 2H]2
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKYPOKY build 20230213Woonghee Lee, Mehdi Rahimi, Yeongjoon Lee and Abigail Chiupeak picking
NMRFAM-SPARKYPOKY build 20230213Woonghee Lee, Mehdi Rahimi, Yeongjoon Lee and Abigail Chiuchemical shift assignment
CNSARIA2.3Wolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Therese E. Malliavin and Michael Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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