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Yorodumi- PDB-2vqv: Structure of HDAC4 catalytic domain with a gain-of-function mutat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vqv | ||||||
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Title | Structure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor | ||||||
Components | HISTONE DEACETYLASE 4 | ||||||
Keywords | HYDROLASE / INHIBITOR / REPRESSOR / CHROMATIN / COILED COIL / HISTONE DEACETYLASE / TRANSCRIPTION REGULATION / UBL CONJUGATION / CHROMATIN REGULATOR / POLYMORPHISM / TRANSCRIPTION / PHOSPHOPROTEIN / HDAC / ZINC / HDACI / NUCLEUS / CYTOPLASM | ||||||
Function / homology | Function and homology information 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 / negative regulation of transcription by competitive promoter binding / regulation of protein 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 / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase / protein lysine deacetylase activity / negative regulation of glycolytic process / SUMO transferase activity / histone deacetylase activity / negative regulation of gene expression, epigenetic / B cell activation / type I interferon-mediated signaling pathway / Notch-HLH transcription pathway / potassium ion binding / protein sumoylation / histone deacetylase complex / RUNX3 regulates p14-ARF / 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 / histone deacetylase binding / positive regulation of DNA-binding transcription factor activity / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
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. ...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. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vqv.cif.gz | 146.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vqv.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vqv ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vqv | HTTPS FTP |
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-Related structure data
Related structure data | 2vqjSC 2vqmC 2vqoC 2vqqC 2vqwC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 9 - 402 / Label seq-ID: 9 - 402
NCS oper: (Code: given Matrix: (-0.29, -0.011, 0.957), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44438.301 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 648-1057 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-11 (OBTAINED FROM EMBL-HEIDELBERG) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56524 |
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-Non-polymers , 5 types, 17 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 669 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 700 TO ALA ...ENGINEERED |
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Sequence details | FIRST THREE RESIDUES OF THE SEQUENCE (GAM) COME FROM CLONING ARTEFACT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M MES PH 6.5, 1.6M AMMONIUM SULPHATE, 10% DIOXANE 1MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. obs: 12577 / % possible obs: 98.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VQJ Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.846 / SU B: 28.082 / SU ML: 0.473 / Cross valid method: THROUGHOUT / ESU R Free: 0.615 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES DUE TO LACK OF ELECTRON DENSITY IN BOTH CHAINS A AND B INCLUDE 21-33 AND 84-114.
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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: 31.45 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→30 Å
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Refine LS restraints |
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