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Yorodumi- PDB-5nwx: Insight into the molecular recognition mechanism of the coactivat... -
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-Basic information
Entry | Database: PDB / ID: 5nwx | ||||||
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Title | Insight into the molecular recognition mechanism of the coactivator NCoA1 by STAT6 | ||||||
Components |
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Keywords | TRANSCRIPTION / NcoA1 / STAT6 / PAS-B domain / transactivation domain | ||||||
Function / homology | Function and homology information regulation of mast cell proliferation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / mammary gland morphogenesis / SUMOylation of transcription cofactors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts / cellular response to reactive nitrogen species ...regulation of mast cell proliferation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / mammary gland morphogenesis / SUMOylation of transcription cofactors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts / cellular response to reactive nitrogen species / negative regulation of type 2 immune response / positive regulation of isotype switching to IgE isotypes / Endogenous sterols / HATs acetylate histones / T-helper 1 cell lineage commitment / STAT6-mediated induction of chemokines / Regulation of lipid metabolism by PPARalpha / isotype switching to IgE isotypes / Cytoprotection by HMOX1 / interleukin-4-mediated signaling pathway / Estrogen-dependent gene expression / nuclear retinoic acid receptor binding / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / mammary gland epithelial cell proliferation / hypothalamus development / male mating behavior / cell surface receptor signaling pathway via JAK-STAT / estrous cycle / cellular response to Thyroglobulin triiodothyronine / growth hormone receptor signaling pathway via JAK-STAT / nuclear retinoid X receptor binding / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / lactation / cerebellum development / Downstream signal transduction / nuclear receptor coactivator activity / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mRNA transcription by RNA polymerase II / defense response / transcription coactivator binding / cerebral cortex development / response to peptide hormone / cellular response to hydrogen peroxide / cytokine-mediated signaling pathway / RNA polymerase II transcription regulator complex / male gonad development / response to estradiol / positive regulation of cold-induced thermogenesis / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / transcription regulator complex / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / chromatin / protein-containing complex binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Russo, L. / Giller, K. / Pfitzner, E. / Griesinger, C. / Becker, S. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Insight into the molecular recognition mechanism of the coactivator NCoA1 by STAT6. Authors: Russo, L. / Giller, K. / Pfitzner, E. / Griesinger, C. / Becker, S. #1: Journal: Journal of Molecular Biology / Year: 2004 Title: Structure of the NCoA-1/SRC-1 PAS-B Domain Bound to the LXXLL Motif of the STAT6 Transactivation domain Authors: Razeto, A. / Ramakrishnan, V. / Litterst, C.M. / Giller, K. / Griesinger, C. / Carlomagno, T. / Lakomek, N. / Heimburg, T. / Lodrini, M. / Pfitzner, E. / Becker, S. #2: Journal: Acta Crystallographica Section D / Year: 2004 Title: Crystallization and preliminary crystallographic studies of the NCoA-1/SRC-1 PAS-B domain bound to the LXXLL motif of the STAT6 transactivation domain Authors: Razeto, A. / Pfitzner, E. / Becker, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nwx.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nwx.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 5nwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/5nwx ftp://data.pdbj.org/pub/pdb/validation_reports/nw/5nwx | HTTPS FTP |
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-Related structure data
Related structure data | 5nwmC 1oj5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14811.774 Da / Num. of mol.: 1 / Fragment: UNP residues 257-385 / Mutation: K343R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ncoa1, Src1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70365, histone acetyltransferase |
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#2: Protein/peptide | Mass: 3452.837 Da / Num. of mol.: 1 / Fragment: UNP residues 783-814 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STAT6 / Production host: synthetic construct (others) / References: UniProt: P42226 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 44.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, 30% PEG 8000, 5% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→53.37 Å / Num. obs: 5471 / % possible obs: 99.8 % / Redundancy: 20.51 % / Rrim(I) all: 0.0246 / Net I/σ(I): 30.26 |
Reflection shell | Resolution: 2.51→2.61 Å / Redundancy: 19.92 % / Mean I/σ(I) all: 6.08 / Rrim(I) all: 0.1315 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OJ5 Resolution: 2.51→53.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.917 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.248 / Stereochemistry target values: Maximum likelihood / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.36 Å2
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Refinement step | Cycle: 1 / Resolution: 2.51→53.37 Å
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