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- PDB-1sse: Solution structure of the oxidized form of the Yap1 redox domain -

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Basic information

Entry
Database: PDB / ID: 1sse
TitleSolution structure of the oxidized form of the Yap1 redox domain
Components(AP-1 like transcription factor YAP1) x 2
KeywordsTRANSCRIPTION ACTIVATOR / disulfide bond / nuclear export signal / NES / redox-regulation
Function / homology
Function and homology information


: / regulation of endoplasmic reticulum unfolded protein response / response to singlet oxygen / response to xenobiotic stimulus => GO:0009410 / : / response to metal ion / response to cadmium ion / response to heat / DNA-binding transcription factor activity / DNA binding ...: / regulation of endoplasmic reticulum unfolded protein response / response to singlet oxygen / response to xenobiotic stimulus => GO:0009410 / : / response to metal ion / response to cadmium ion / response to heat / DNA-binding transcription factor activity / DNA binding / nucleus / cytoplasm
Similarity search - Function
YAP1 redox domain. Chain B / Transcription factor PAP1 / Yap1 redox domain superfamily / Transcription factor PAP1 / bZIP transcription factor / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Recoverin; domain 1 ...YAP1 redox domain. Chain B / Transcription factor PAP1 / Yap1 redox domain superfamily / Transcription factor PAP1 / bZIP transcription factor / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AP-1-like transcription factor YAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsWood, M.J. / Storz, G. / Tjandra, N.
CitationJournal: Nature / Year: 2004
Title: Structural basis for redox regulation of Yap1 transcription factor localization.
Authors: Wood, M.J. / Storz, G. / Tjandra, N.
History
DepositionMar 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-1 like transcription factor YAP1
B: AP-1 like transcription factor YAP1


Theoretical massNumber of molelcules
Total (without water)13,5852
Polymers13,5852
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)20 / 100Stuctures with the lowest energy and no NOE or dihedral violations > 0.5 A and 5 degrees, respectively.
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide AP-1 like transcription factor YAP1 / Phenanthroline resistance protein PAR1 / Pleiotropic drug resistance protein PDR4


Mass: 4128.429 Da / Num. of mol.: 1 / Fragment: n-CRD, residues 279-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YAP1, SNQ3, PAR1, PDR4, YML007W, YM9571.12 / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19880
#2: Protein AP-1 like transcription factor YAP1 / Phenanthroline resistance protein PAR1 / Pleiotropic drug resistance protein PDR4


Mass: 9456.393 Da / Num. of mol.: 1 / Fragment: c-CRD, residues 565-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YAP1, SNQ3, PAR1, PDR4, YML007W, YM9571.12 / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19880

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1214D 13C/15N-separated NOESY
131HN(CA)CB
141Experiments for residual dipolar coupling measurements
1524D 13C-separated NOESY
NMR detailsText: Residual dipolar couplings (DN-H and DCaH) were measured in a solution composed of PF1 phage.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM U-15N; U-15N & 13C.10 mM NaPhos, 20 mM NaCL, 10% D2O
20.8 mM U-15N & 13C.10 mM NaPhos, 20 mM NaCL, 100% D2O
Sample conditionsIonic strength: 20 mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 303 K

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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 AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1processing
PIPP4.2.8processing
XwinNMR2.5collection
XPLOR-NIH2.0.6Brunger & SCHWIETERS, KUSZEWSKI, TJANDRA, CLORErefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: Yap1-RD structures were calculated with 1103 NOE distance restraints, 54 hydrogen bond restraints, 92 dihedral angle restraints and 93 residual dipolar couplings. Residues 279-300 and 565-592 are disordered.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Stuctures with the lowest energy and no NOE or dihedral violations > 0.5 A and 5 degrees, respectively.
Conformers calculated total number: 100 / Conformers submitted total number: 20

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