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Yorodumi- PDB-1tqe: Mechanism of recruitment of class II histone deacetylases by myoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tqe | ||||||
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Title | Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2 | ||||||
Components |
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Keywords | TRANSCRIPTION/PROTEIN BINDING/DNA / MEF2 / HDAC / co-repressor / transcription / TRANSCRIPTION-PROTEIN BINDING-DNA COMPLEX | ||||||
Function / homology | Function and homology information regulation of striated muscle cell differentiation / : / negative regulation of cytokine production => GO:0001818 / : / histone H4K16 deacetylase activity / : / regulation of skeletal muscle fiber development / DNA-binding transcription factor binding => GO:0140297 / : / negative regulation of lipoprotein lipase activity ...regulation of striated muscle cell differentiation / : / negative regulation of cytokine production => GO:0001818 / : / histone H4K16 deacetylase activity / : / regulation of skeletal muscle fiber development / DNA-binding transcription factor binding => GO:0140297 / : / negative regulation of lipoprotein lipase activity / negative regulation of striated muscle tissue development / peptidyl-lysine deacetylation / histone deacetylase / protein lysine deacetylase activity / muscle organ development / histone methyltransferase complex / positive regulation of cell migration involved in sprouting angiogenesis / histone deacetylase activity / B cell activation / Myogenesis / transcription factor binding / histone deacetylase complex / B cell differentiation / cholesterol homeostasis / determination of adult lifespan / protein kinase C binding / histone deacetylase binding / cellular response to insulin stimulus / transcription corepressor activity / sequence-specific double-stranded DNA binding / cell junction / chromatin organization / nervous system development / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Chen, L. / Han, A. / He, J. / Wu, Y. / Liu, J.O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Mechanism of Recruitment of Class II Histone Deacetylases by Myocyte Enhancer Factor-2. Authors: Han, A. / He, J. / Wu, Y. / Liu, J.O. / Chen, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tqe.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tqe.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tqe_validation.pdf.gz | 471.1 KB | Display | wwPDB validaton report |
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Full document | 1tqe_full_validation.pdf.gz | 505.3 KB | Display | |
Data in XML | 1tqe_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 1tqe_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/1tqe ftp://data.pdbj.org/pub/pdb/validation_reports/tq/1tqe | HTTPS FTP |
-Related structure data
Related structure data | 1egwS 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
#1: DNA chain | Mass: 5218.437 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 5191.394 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 11038.855 Da / Num. of mol.: 4 / Fragment: residues 1-93 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q02080 #4: Protein/peptide | Mass: 2769.174 Da / Num. of mol.: 2 / Fragment: residues 138-158 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q99N13 |
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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: 2.54 Å3/Da / Density % sol: 49.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 315 K / Method: vapor diffusion, hanging drop / pH: 6.35 Details: BTP, PEG, NaCl, glycerol, MgCl2, CaCl2, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 315K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 18, 2003 / Details: mirrors |
Radiation | Monochromator: Ni Mirror and Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 19058 / Num. obs: 17405 / % possible obs: 91.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Rsym value: 0.034 / Net I/σ(I): 63 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1823 / Rsym value: 0.124 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Structure of MEF2A and DNA complex, pdb entry 1egw Resolution: 2.7→30 Å / Isotropic thermal model: anisotropic / Cross valid method: throughtout / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Displacement parameters | Biso mean: 88.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.452 / Rfactor Rwork: 0.445 / Total num. of bins used: 6
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Xplor file |
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