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- PDB-2vqw: Structure of inhibitor-free HDAC4 catalytic domain (with gain-of-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vqw | ||||||
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Title | Structure of inhibitor-free HDAC4 catalytic domain (with gain-of- function mutation His332Tyr) | ||||||
![]() | HISTONE DEACETYLASE 4 | ||||||
![]() | HYDROLASE / INHIBITOR / REPRESSOR / CHROMATIN / COILED COIL / HISTONE DEACETYLASE / TRANSCRIPTION REGULATION / UBL CONJUGATION / CHROMATIN REGULATOR / POLYMORPHISM / TRANSCRIPTION / PHOSPHOPROTEIN / HDAC / ZINC / HDACI / NUCLEUS / CYTOPLASM | ||||||
Function / homology | ![]() RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / regulation of protein binding / negative regulation of transcription by competitive promoter binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase ...RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / regulation of protein binding / negative regulation of transcription by competitive promoter binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase / protein lysine deacetylase activity / negative regulation of glycolytic process / SUMO transferase activity / negative regulation of gene expression, epigenetic / histone deacetylase activity / type I interferon-mediated signaling pathway / B cell activation / Notch-HLH transcription pathway / potassium ion binding / RUNX3 regulates p14-ARF / histone deacetylase complex / protein sumoylation / transcription repressor complex / SUMOylation of chromatin organization proteins / response to interleukin-1 / B cell differentiation / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of DNA-binding transcription factor activity / histone deacetylase binding / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / nuclear speck / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bottomley, M.J. / Lo Surdo, P. / Di Giovine, P. / Cirillo, A. / Scarpelli, R. / Ferrigno, F. / Jones, P. / Neddermann, P. / De Francesco, R. / Steinkuhler, C. ...Bottomley, M.J. / Lo Surdo, P. / Di Giovine, P. / Cirillo, A. / Scarpelli, R. / Ferrigno, F. / Jones, P. / Neddermann, P. / De Francesco, R. / Steinkuhler, C. / Gallinari, P. / Carfi, A. | ||||||
![]() | ![]() Title: Structural and Functional Analysis of the Human Hdac4 Catalytic Domain Reveals a Regulatory Structural Zinc-Binding Domain. Authors: Bottomley, M.J. / Lo Surdo, P. / Di Giovine, P. / Cirillo, A. / Scarpelli, R. / Ferrigno, F. / Jones, P. / Neddermann, P. / De Francesco, R. / Steinkuhler, C. / Gallinari, P. / Carfi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.6 KB | Display | ![]() |
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PDB format | ![]() | 62.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.4 KB | Display | ![]() |
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Full document | ![]() | 428.7 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vqjSC ![]() 2vqmC ![]() 2vqoC ![]() 2vqqC ![]() 2vqvC 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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Unit cell |
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Components
#1: Protein | Mass: 44502.430 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 648-1057 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.9 Å3/Da / Density % sol: 71 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1M HEPES PH 7.5, 18% PEG 10000, 1MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 3→60 Å / Num. obs: 15460 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3→3.48 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VQJ Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / SU B: 17.23 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 0.702 / ESU R Free: 0.356 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.6 Å2
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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