+Open data
-Basic information
Entry | Database: PDB / ID: 1sse | ||||||
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Title | Solution structure of the oxidized form of the Yap1 redox domain | ||||||
Components | (AP-1 like transcription factor YAP1) x 2 | ||||||
Keywords | TRANSCRIPTION 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 | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Wood, M.J. / Storz, G. / Tjandra, N. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Structural basis for redox regulation of Yap1 transcription factor localization. Authors: Wood, M.J. / Storz, G. / Tjandra, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sse.cif.gz | 708.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sse.ent.gz | 613.7 KB | Display | PDB format |
PDBx/mmJSON format | 1sse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/1sse ftp://data.pdbj.org/pub/pdb/validation_reports/ss/1sse | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein/peptide | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Residual dipolar couplings (DN-H and DCaH) were measured in a solution composed of PF1 phage. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 20 mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer 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 |