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Yorodumi- PDB-5x07: Crystal structure of FOXA2 DNA binding domain bound to a full con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x07 | ||||||||||||
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Title | Crystal structure of FOXA2 DNA binding domain bound to a full consensus DNA site | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / FOXA2 / Forkhead domain / Consensus binding site / Isothermal Titration Calorimetry / ITC / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information negative regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of glucokinase activity / positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of transcription from RNA polymerase II promoter by glucose / positive regulation of embryonic development / response to interleukin-6 / endocrine pancreas development / negative regulation of epithelial to mesenchymal transition / regulation of insulin secretion involved in cellular response to glucose stimulus ...negative regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of glucokinase activity / positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of transcription from RNA polymerase II promoter by glucose / positive regulation of embryonic development / response to interleukin-6 / endocrine pancreas development / negative regulation of epithelial to mesenchymal transition / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm / positive regulation of gastrulation / Formation of axial mesoderm / dopaminergic neuron differentiation / cell fate specification / regulation of blood coagulation / Regulation of gene expression in beta cells / anatomical structure morphogenesis / adult locomotory behavior / negative regulation of DNA-binding transcription factor activity / sequence-specific double-stranded DNA binding / cell junction / chromatin organization / nucleic acid binding / cell differentiation / 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 / protein domain specific binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 Å | ||||||||||||
Authors | Li, J. / Guo, M. / Zhou, Z. / Jiang, L. / Chen, X. / Qu, L. / Wu, D. / Chen, Z. / Chen, L. / Chen, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Biochemistry / Year: 2017 Title: Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site Authors: Li, J. / Machado, A.C.D. / Guo, M. / Sagendorf, J.M. / Zhou, Z. / Jiang, L. / Chen, X. / Wu, D. / Qu, L. / Chen, Z. / Chen, L. / Rohs, R. / Chen, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x07.cif.gz | 278.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x07.ent.gz | 232.5 KB | Display | PDB format |
PDBx/mmJSON format | 5x07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/5x07 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/5x07 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4860.159 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: DNA chain | Mass: 4932.272 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Protein | Mass: 12392.217 Da / Num. of mol.: 4 / Fragment: UNP residues 157-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FOXA2, HNF3B, TCF3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y261 |
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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: 2.78 Å3/Da / Density % sol: 55.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 80mM Mg (OAc)2, 50mM MES buffer, 16%-20% PEG4K, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.796→33.64 Å / Num. obs: 178752 / % possible obs: 96.8 % / Redundancy: 7.5 % / Net I/σ(I): 19.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.796→33.637 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.796→33.637 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 178.8931 Å / Origin y: 40.393 Å / Origin z: 185.4466 Å
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Refinement TLS group | Selection details: all |