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- PDB-3c0y: Crystal structure of catalytic domain of human histone deacetylas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c0y | |||||||||
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Title | Crystal structure of catalytic domain of human histone deacetylase HDAC7 | |||||||||
![]() | Histone deacetylase 7a | |||||||||
![]() | HYDROLASE / HISTONE DEACETYLASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / Chromatin regulator / Cytoplasm / Nucleus / Phosphoprotein / Polymorphism / Repressor / Transcription / Transcription regulation | |||||||||
Function / homology | ![]() regulation of mRNA processing / protein deacetylation / histone deacetylase / protein lysine deacetylase activity / SUMO transferase activity / cell-cell junction assembly / negative regulation of non-canonical NF-kappaB signal transduction / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of interleukin-2 production / positive regulation of cell migration involved in sprouting angiogenesis ...regulation of mRNA processing / protein deacetylation / histone deacetylase / protein lysine deacetylase activity / SUMO transferase activity / cell-cell junction assembly / negative regulation of non-canonical NF-kappaB signal transduction / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of interleukin-2 production / positive regulation of cell migration involved in sprouting angiogenesis / histone deacetylase activity / Notch-HLH transcription pathway / histone deacetylase complex / protein sumoylation / negative regulation of osteoblast differentiation / vasculogenesis / SUMOylation of DNA damage response and repair proteins / 14-3-3 protein binding / Regulation of PTEN gene transcription / protein kinase C binding / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription corepressor activity / DNA-binding transcription factor binding / chromatin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Min, J.R. / Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Kwiatkowski, N.P. / Mazitschek, R. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Min, J.R. / Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Kwiatkowski, N.P. / Mazitschek, R. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC) | |||||||||
![]() | ![]() Title: Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity. Authors: Schuetz, A. / Min, J. / Allali-Hassani, A. / Schapira, M. / Shuen, M. / Loppnau, P. / Mazitschek, R. / Kwiatkowski, N.P. / Lewis, T.A. / Maglathin, R.L. / McLean, T.H. / Bochkarev, A. / ...Authors: Schuetz, A. / Min, J. / Allali-Hassani, A. / Schapira, M. / Shuen, M. / Loppnau, P. / Mazitschek, R. / Kwiatkowski, N.P. / Lewis, T.A. / Maglathin, R.L. / McLean, T.H. / Bochkarev, A. / Plotnikov, A.N. / Vedadi, M. / Arrowsmith, C.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.5 KB | Display | ![]() |
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PDB format | ![]() | 181.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.1 KB | Display | ![]() |
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Full document | ![]() | 481.3 KB | Display | |
Data in XML | ![]() | 44.6 KB | Display | |
Data in CIF | ![]() | 63.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c0zC ![]() 3c10C ![]() 2nvr C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45518.340 Da / Num. of mol.: 3 / Fragment: Catalytic domain: Residues 482-903 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain (production host): BL21(DE3)Codon Plus RIL (Stratagen) References: UniProt: Q8WUI4 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.53 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 13 % PEG 3350, 0.1 M HEPES pH 7.5, 10 % Isopropanol, 1 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 65508 / Num. obs: 64241 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5579 / % possible all: 85.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2NVR ![]() 2nvr Resolution: 2.1→34.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.425 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.494 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→34.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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