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Yorodumi- PDB-4a69: Structure of HDAC3 bound to corepressor and inositol tetraphosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a69 | ||||||
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Title | Structure of HDAC3 bound to corepressor and inositol tetraphosphate | ||||||
Components |
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Keywords | TRANSCRIPTION / HYDROLASE | ||||||
Function / homology | Function and homology information : / : / transcription corepressor binding => GO:0001222 / NAD-dependent histone H3K14 deacetylase activity / NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / p75NTR negatively regulates cell cycle via SC1 / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding ...: / : / transcription corepressor binding => GO:0001222 / NAD-dependent histone H3K14 deacetylase activity / NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / p75NTR negatively regulates cell cycle via SC1 / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / protein deacetylation / negative regulation of JNK cascade / cellular response to fluid shear stress / histone deacetylase / protein lysine deacetylase activity / Notch binding / histone deacetylase activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / RUNX2 regulates osteoblast differentiation / Association of TriC/CCT with target proteins during biosynthesis / transcription factor binding / histone deacetylase complex / Regulation of MECP2 expression and activity / regulation of lipid metabolic process / NF-kappaB binding / estrous cycle / positive regulation of TOR signaling / spindle assembly / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / : / transcription repressor complex / lactation / Regulation of lipid metabolism by PPARalpha / cyclin binding / cerebellum development / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / circadian regulation of gene expression / regulation of protein stability / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / positive regulation of protein import into nucleus / circadian rhythm / transcription corepressor activity / Circadian Clock / response to estradiol / chromatin organization / positive regulation of cold-induced thermogenesis / nuclear body / positive regulation of protein phosphorylation / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of apoptotic process / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Watson, P.J. / Fairall, L. / Santos, G.M. / Schwabe, J.W.R. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Structure of Hdac3 Bound to Co-Repressor and Inositol Tetraphosphate. Authors: Watson, P.J. / Fairall, L. / Santos, G.M. / Schwabe, J.W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a69.cif.gz | 196.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a69.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 4a69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/4a69 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a69 | HTTPS FTP |
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-Related structure data
Related structure data | 3ew8S 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 42916.484 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: O15379, histone deacetylase #2: Protein | Mass: 11309.239 Da / Num. of mol.: 2 / Fragment: RESIDUES 389-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y618 |
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-Non-polymers , 6 types, 361 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M HEPES PH 7.5 0.2 M NACL 10 % V/V PROPAN-2-OL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 |
Detector | Type: PILATUS 2D HYBRID ARRAY / Detector: PIXEL / Date: May 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→28.93 Å / Num. obs: 49237 / % possible obs: 85.9 % / Observed criterion σ(I): 2.7 / Redundancy: 2.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.06→2.17 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / % possible all: 68.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EW8 Resolution: 2.06→95.35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.675 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.739 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→95.35 Å
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