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- PDB-1k5r: YAP65 WW domain S24-Amino-Ethylsulfanyl-Acetic Acid mutant -

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Basic information

Entry
Database: PDB / ID: 1k5r
TitleYAP65 WW domain S24-Amino-Ethylsulfanyl-Acetic Acid mutant
Components
  • 65 KDA YES-ASSOCIATED PROTEIN
  • Fragment of WBP-1
KeywordsSIGNALING PROTEIN / WW domain / YAP65 / beta-sheet proteins / stability of beta sheets
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 / WW domain binding / 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 / interleukin-6-mediated signaling pathway / positive regulation of stem cell population maintenance / 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-binding protein 1-like / WW domain-binding protein 1 / 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 / WW domain-binding protein 1
Similarity search - Component
MethodSOLUTION NMR / simulated anneling
AuthorsFerguson, N. / Pires, J.R. / Toepert, F. / Johnson, C.M. / Pan, Y.P. / Volkmer-Engert, R. / Schneider-Mergener, J. / Daggett, V. / Oschkinat, H. / Fersht, A.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions.
Authors: Ferguson, N. / Pires, J.R. / Toepert, F. / Johnson, C.M. / Pan, Y.P. / Volkmer-Engert, R. / Schneider-Mergener, J. / Daggett, V. / Oschkinat, H. / Fersht, A.
History
DepositionOct 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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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: Fragment of WBP-1


Theoretical massNumber of molelcules
Total (without water)5,6952
Polymers5,6952
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide 65 KDA YES-ASSOCIATED PROTEIN / YAP65 / yes-associated protein 65 kDa


Mass: 4710.266 Da / Num. of mol.: 1 / Fragment: WW domain, residues 5-44 / Mutation: S24/Amino-ethyl-sulfanyl-acetic acid / Source method: obtained synthetically / Details: The sequence occurs naturally in humans / References: UniProt: P46937
#2: Protein/peptide Fragment of WBP-1


Mass: 985.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The sequence occurs naturally in humans / References: 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
1222D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1phosphate buffer 10 mM, Nacl 100mM, DTT 0.1mM, EDTA 0.1 mM, pH 6, WW domain 1.2 mM Ligand 2.4 mMH20 (10% D20)
2phosphate buffer 10 mM, Nacl 100mM, DTT 0.1mM, EDTA 0.1 mM, pH 6 WW domain, 1.2 mM Ligand 2.4 mMD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 6 1 atm288 K
2100 mM 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERprocessing
X-PLOR3.1Brunger, A.T.refinement
ANSIG3.3Kraulis, P.J.data analysis
RefinementMethod: simulated anneling / Software ordinal: 1
Details: 2000K, 200 RUNS, FORCE CONSTANTS FOR NOE 50 KCALMOL-1RAD-2, 590 RESTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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