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- PDB-1k9q: YAP65 WW domain complexed to N-(n-octyl)-GPPPY-NH2 -

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Basic information

Entry
Database: PDB / ID: 1k9q
TitleYAP65 WW domain complexed to N-(n-octyl)-GPPPY-NH2
Components
  • 65 kDa Yes-associated protein
  • WW domain binding protein-1
KeywordsSTRUCTURAL PROTEIN / WW domain / YAP65 / beta-sheet proteins / ligands / proline-rich peptides
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / 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 / tissue homeostasis / hippo signaling / regulation of stem cell proliferation / 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 / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial cell differentiation / negative regulation of fat cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / Nuclear signaling by ERBB4 / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / response to progesterone / epithelial cell proliferation / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / cellular response to gamma radiation / wound healing / cell morphogenesis / positive regulation of protein localization to nucleus / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / cell-cell junction / 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 / cell population proliferation / 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 / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Single Sheet / Mainly Beta
Similarity search - Domain/homology
N-OCTANE / : / Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Simulated anneling
AuthorsPires, J.R. / Taha-Nejad, F. / Toepert, F. / Ast, T. / Hoffmuller, U. / Schneider-Mergener, J. / Kuhne, R. / Macias, M.J. / Oschkinat, H.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structures of the YAP65 WW domain and the variant L30 K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope.
Authors: Pires, J.R. / Taha-Nejad, F. / Toepert, F. / Ast, T. / Hoffmuller, U. / Schneider-Mergener, J. / Kuhne, R. / Macias, M.J. / Oschkinat, H.
History
DepositionOct 30, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 13, 2013Group: Other
Revision 1.5Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 65 kDa Yes-associated protein
B: WW domain binding protein-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3243
Polymers5,2102
Non-polymers1141
Water0
1


  • Idetical with deposited unit
  • defined by author
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/peptide 65 kDa Yes-associated protein / YAP65


Mass: 4682.166 Da / Num. of mol.: 1 / Fragment: Wild type WW domain / Source method: obtained synthetically
Details: This sequence was synthetically obtained, by semiautomated spot synthesis in a cellulose support.
References: UniProt: P46937
#2: Protein/peptide WW domain binding protein-1 / WBP-1


Mass: 527.593 Da / Num. of mol.: 1 / Fragment: residues 149-153 / Mutation: P3G / Source method: obtained synthetically
Details: This sequence was synthetically obtained by spot synthesis in a cellulose support.
Source: (synth.) Homo sapiens (human) / References: GenBank: 4205084
#3: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1phosphate buffer 10mM, NaCl 100mM, DTT 0.1mM, EDTA 0.1mM, pH 6, WW domain 1.2mM, ligand 2.4mMH2O (10% D2O)
2phosphate buffer 10mM, NaCl 100mM, DTT 0.1mM, EDTA 0.1mM, pH 6, WW domain 1.2mM, ligand 2.4mMD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NaCl 6 1 atm288 K
2100mM NaCl 6 1 atm288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
ANSIG3.3Kraulis, P.J.data analysis
X-PLOR3.1Brunger, A.T.refinement
RefinementMethod: Simulated anneling / Software ordinal: 1
Details: 2000K, 200 runs, Force constants for NOE 50kcal mol-1 rad-2, 422 restraints
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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