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- PDB-1jmq: YAP65 (L30K mutant) WW domain in Complex with GTPPPPYTVG peptide -

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Basic information

Entry
Database: PDB / ID: 1jmq
TitleYAP65 (L30K mutant) WW domain in Complex with GTPPPPYTVG peptide
Components
  • 65 KDA YES-ASSOCIATED PROTEIN
  • WW Domain Binding Protein-1
KeywordsSTRUCTURAL PROTEIN / WW domain / polyproline ligand / YAP65 mutant
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 / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / 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 / WW domain binding / negative regulation of epithelial cell differentiation / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of stem cell population maintenance / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / 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 / positive regulation of canonical Wnt signaling pathway / cell junction / 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
WW domain-binding protein 1-like / : / WW domain-binding protein 1 / : / Omega loop, TEAD interating region 3 / : / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / WW domain / WW/rsp5/WWP domain signature. ...WW domain-binding protein 1-like / : / WW domain-binding protein 1 / : / Omega loop, TEAD interating region 3 / : / 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
: / Transcriptional coactivator YAP1 / WW domain-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
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
DepositionJul 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET DETERMINATION METHOD: AUTHOR
Remark 999SEQUENCE THE WW DOMAIN BINDING PROTEIN-1 FRAGMENT WAS CHEMICALLY SYNTHESIZED.

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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
P: WW Domain Binding Protein-1


Theoretical massNumber of molelcules
Total (without water)6,3452
Polymers6,3452
Non-polymers00
Water00
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: 5360.021 Da / Num. of mol.: 1 / Mutation: L30K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YAP65 / Plasmid: pGAT2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46937
#2: Protein/peptide WW Domain Binding Protein-1 / WBP-1


Mass: 985.090 Da / Num. of mol.: 1 / Fragment: residues 147-156 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: GenBank: 4205084, UniProt: Q96G27*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
2322D NOESY
2422D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM WW domain; 2.4 mM peptide GTPPPPYTVG; 10mM potassium phosphate buffer pH6; 100mM NaCl; 0.1 mM DTT; 0.1 mM EDTA,90% H20, 10% D20
21.2 mM WW domain; 2.4 mM peptide GTPPPPYTVG; 10mM potassium phosphate buffer pH6; 100mM NaCl; 0.1 mM DTT; 0.1 mM EDTA,100%D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NaCl 61 atm288 K
2100mM NaCl 61 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
XwinNMR2.6BRUKER, A.G.processing
XwinNMR2.6BRUKER, A.G.collection
ANSIG3.3Kraulis, P.Jdata analysis
X-PLOR3.1Brunger, A.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 2000K, 200 runs, force constants for NOE 50 kcalmol-1rad-2, 590 restraints including 20 hydrogen bond 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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