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- PDB-7yze: Crystal structure of the human FoxA2 bound to the TGTTTACT site (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yze | |||||||||
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Title | Crystal structure of the human FoxA2 bound to the TGTTTACT site (forkhead motif GTAAACA) | |||||||||
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![]() | DNA BINDING PROTEIN / transcription factor | |||||||||
Function / homology | ![]() negative regulation of transcription from RNA polymerase II promoter by glucose / positive regulation of cell-cell adhesion mediated by cadherin / negative regulation of glucokinase activity / primitive streak formation / positive regulation of embryonic development / positive regulation of transcription from RNA polymerase II promoter by glucose / response to interleukin-6 / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm ...negative regulation of transcription from RNA polymerase II promoter by glucose / positive regulation of cell-cell adhesion mediated by cadherin / negative regulation of glucokinase activity / primitive streak formation / positive regulation of embryonic development / positive regulation of transcription from RNA polymerase II promoter by glucose / response to interleukin-6 / endocrine pancreas development / 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 / negative regulation of epithelial to mesenchymal transition / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pluta, R. / Macias, M.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1. Authors: Pluta, R. / Aragon, E. / Prescott, N.A. / Ruiz, L. / Mees, R.A. / Baginski, B. / Flood, J.R. / Martin-Malpartida, P. / Massague, J. / David, Y. / Macias, M.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.4 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 566.5 KB | Display | ![]() |
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Full document | ![]() | 567 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yz7C ![]() 7yzaC ![]() 7yzbC ![]() 7yzcC ![]() 7yzdC ![]() 7yzfC ![]() 7yzgC ![]() 5x07S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14652.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4952.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 4841.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 3 types, 30 molecules ![](data/chem/img/K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-K / |
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#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.985→46.185 Å / Num. obs: 15071 / % possible obs: 93.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rpim(I) all: 0.012 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.985→2.126 Å / Num. unique obs: 756 / CC1/2: 0.573 / Rpim(I) all: 0.584 / % possible all: 53.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5x07 Resolution: 1.99→46.18 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.26 / 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 max: 135.32 Å2 / Biso mean: 67.4917 Å2 / Biso min: 43.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.99→46.18 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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