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Yorodumi- PDB-4m9e: Structure of Klf4 zinc finger DNA binding domain in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 4m9e | ||||||
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Title | Structure of Klf4 zinc finger DNA binding domain in complex with methylated DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / DNA methylation / transcription factor / cellular reprogramming / C2H2 Zinc finger / DNA binding / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information negative regulation of leukocyte adhesion to arterial endothelial cell / cellular response to cycloheximide / regulation of blastocyst development / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of hemoglobin biosynthetic process / negative regulation of response to cytokine stimulus / post-embryonic camera-type eye development / glandular epithelial cell differentiation / epidermal cell differentiation ...negative regulation of leukocyte adhesion to arterial endothelial cell / cellular response to cycloheximide / regulation of blastocyst development / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of hemoglobin biosynthetic process / negative regulation of response to cytokine stimulus / post-embryonic camera-type eye development / glandular epithelial cell differentiation / epidermal cell differentiation / negative regulation of muscle hyperplasia / epidermis morphogenesis / negative regulation of heterotypic cell-cell adhesion / cellular response to peptide / negative regulation of interleukin-8 production / phosphatidylinositol 3-kinase regulator activity / regulation of axon regeneration / cellular response to laminar fluid shear stress / post-embryonic hemopoiesis / negative regulation of cell migration involved in sprouting angiogenesis / defense response to tumor cell / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / positive regulation of sprouting angiogenesis / fat cell differentiation / regulation of cell differentiation / somatic stem cell population maintenance / epidermis development / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / establishment of skin barrier / cellular response to retinoic acid / response to retinoic acid / negative regulation of angiogenesis / negative regulation of cell migration / : / cellular response to leukemia inhibitory factor / transcription coregulator binding / promoter-specific chromatin binding / negative regulation of smooth muscle cell proliferation / euchromatin / negative regulation of ERK1 and ERK2 cascade / chromatin DNA binding / cellular response to growth factor stimulus / beta-catenin binding / positive regulation of miRNA transcription / histone deacetylase binding / cellular response to hydrogen peroxide / microtubule cytoskeleton / positive regulation of nitric oxide biosynthetic process / regulation of cell population proliferation / gene expression / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å | ||||||
Authors | Liu, Y. / Olanrewaju, Y.O. / Blumenthal, R.M. / Zhang, X. / Cheng, X. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Structural basis for Klf4 recognition of methylated DNA. Authors: Liu, Y. / Olanrewaju, Y.O. / Zheng, Y. / Hashimoto, H. / Blumenthal, R.M. / Zhang, X. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m9e.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m9e.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 4m9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m9e_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 4m9e_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | 4m9e_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4m9e_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/4m9e ftp://data.pdbj.org/pub/pdb/validation_reports/m9/4m9e | HTTPS FTP |
-Related structure data
Related structure data | 2wbuS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 10428.806 Da / Num. of mol.: 1 / Fragment: UNP residues 396-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klf4, Ezf, Gklf, Zie / Plasmid: pXC1248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60793 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3140.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesis |
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#3: DNA chain | Mass: 2979.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesis |
-Non-polymers , 4 types, 139 molecules
#4: Chemical | ChemComp-GOL / | ||
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#5: Chemical | ChemComp-ACT / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, 0.25M NaCl and 20% polyethylene glycol 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2013 Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: double crystal - liqued nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→70 Å / Num. obs: 13918 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 26.42 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1103 / % possible all: 80.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WBU Resolution: 1.851→34.44 Å / SU ML: 0.18 / Isotropic thermal model: FLAT BULK SOLVENT MODEL / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.851→34.44 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: 53.3137 Å / Origin y: 72.266 Å / Origin z: 141.9154 Å
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Refinement TLS group | Selection details: all |