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Basic information

Entry
Database: PDB / ID: 2l4j
TitleYap ww2
ComponentsYes-associated protein 2 (YAP2)
KeywordsTRANSCRIPTION / WW domain / YAP / Medaka
Function / homology
Function and homology information


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
Yes-associated protein 2 (YAP2)
Similarity search - Component
Biological speciesOryzias latipes (Japanese medaka)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average, model 1
AuthorsWebb, C. / Upadhyay, A. / Furutani-Seiki, M. / Bagby, S.
CitationJournal: Biochemistry / Year: 2011
Title: Structural Features and Ligand Binding Properties of Tandem WW Domains from YAP and TAZ, Nuclear Effectors of the Hippo Pathway.
Authors: Webb, C. / Upadhyay, A. / Giuntini, F. / Eggleston, I. / Furutani-Seiki, M. / Ishima, R. / Bagby, S.
History
DepositionOct 7, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Yes-associated protein 2 (YAP2)


Theoretical massNumber of molelcules
Total (without water)5,1311
Polymers5,1311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: Protein/peptide Yes-associated protein 2 (YAP2) / 2nd WW domain of Yes-associated protein 2


Mass: 5130.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Plasmid: pSV281 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7FH70*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the second WW domain of YAP from medaka fish.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N TOCSY
1313D 1H-15N NOESY
1423D CBCA(CO)NH
1523D HNCO
1623D HN(CA)CB
1723D C(CO)NH
1823D HN(CO)CA
1923D (H)CCH-COSY
11023D (H)CCH-TOCSY
11113D HNHA
11223D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM potassium phosphate, 200 mM sodium chloride, 5 mM EDTA, 400-600 mM [U-15N] YAP WW2 protein, 93% H2O/7% D2O93% H2O/7% D2O
250 mM potassium phosphate, 200 mM sodium chloride, 5 mM EDTA, 400-600 mM [U-13C; U-15N] YAP WW2 protein, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
50 mMpotassium phosphate-11
200 mMsodium chloride-21
5 mMEDTA-31
mMYAP WW2 protein-4[U-15N]400-6001
50 mMpotassium phosphate-52
200 mMsodium chloride-62
5 mMEDTA-72
mMYAP WW2 protein-8[U-13C; U-15N]400-6002
Sample conditionsIonic strength: 0.2 / pH: 5.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian Unity INOVA / Manufacturer: Varian / Model: Unity INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPN_AnalysisCCPNchemical shift assignment
CCPN_AnalysisCCPNdata analysis
CCPN_AnalysisCCPNpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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