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- PDB-7yzf: Crystal structure of the human FoxA2 bound to the TGTTTATT site (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yzf | |||||||||
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Title | Crystal structure of the human FoxA2 bound to the TGTTTATT site (forkhead motif ATAAACA) | |||||||||
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![]() | DNA BINDING PROTEIN / transcription factor | |||||||||
Function / homology | ![]() 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 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 / negative regulation of glucokinase activity / positive regulation of cell-cell adhesion mediated by cadherin / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / 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 | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7yz7C ![]() 7yzaC ![]() 7yzbC ![]() 7yzcC ![]() 7yzdC ![]() 7yzeSC ![]() 7yzgC 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
#1: DNA chain | Mass: 4967.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: DNA chain | Mass: 4825.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Protein | Mass: 14652.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 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: 2.179→58.421 Å / Num. obs: 9215 / % possible obs: 86.5 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rpim(I) all: 0.018 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.179→2.378 Å / Num. unique obs: 462 / CC1/2: 0.593 / Rpim(I) all: 0.544 / % possible all: 52.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7YZE Resolution: 2.18→58.42 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 18.039 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→58.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.236 Å
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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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