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- PDB-7yza: Crystal structure of the zebrafish FoxH1 bound to the TGTGTATT site -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yza | |||||||||
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Title | Crystal structure of the zebrafish FoxH1 bound to the TGTGTATT site | |||||||||
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![]() | DNA BINDING PROTEIN / transcription factor | |||||||||
Function / homology | ![]() prechordal plate formation / axial mesoderm morphogenesis / specification of animal organ position / axial mesodermal cell fate specification / floor plate formation / lens placode formation involved in camera-type eye formation / Spemann organizer formation at the embryonic shield / floor plate development / somite rostral/caudal axis specification / embryonic heart tube left/right pattern formation ...prechordal plate formation / axial mesoderm morphogenesis / specification of animal organ position / axial mesodermal cell fate specification / floor plate formation / lens placode formation involved in camera-type eye formation / Spemann organizer formation at the embryonic shield / floor plate development / somite rostral/caudal axis specification / embryonic heart tube left/right pattern formation / mesendoderm development / activin responsive factor complex / cell migration involved in gastrulation / endoderm formation / regulation of BMP signaling pathway / notochord formation / notochord development / embryonic heart tube morphogenesis / brain morphogenesis / dorsal/ventral pattern formation / determination of left/right symmetry / hypothalamus development / blood vessel development / heart looping / SMAD binding / cellular response to cytokine stimulus / mesoderm formation / anatomical structure morphogenesis / transforming growth factor beta receptor signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA 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 / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus 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 | ![]() | 132 KB | Display | ![]() |
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PDB format | ![]() | 100 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425 KB | Display | ![]() |
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Full document | ![]() | 425.1 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yz7SC ![]() 7yzbC ![]() 7yzcC ![]() 7yzdC ![]() 7yzeC ![]() 7yzfC ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14482.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 4992.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: DNA chain | Mass: 4801.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 41% PEG Smear LOW |
-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: Jul 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→46.78 Å / Num. obs: 57653 / % possible obs: 85.1 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.02 / Rrim(I) all: 0.037 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.18→1.239 Å / Redundancy: 2.5 % / Num. unique obs: 3026 / CC1/2: 0.407 / Rpim(I) all: 0.627 / % possible all: 41.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7yz7 Resolution: 1.18→46.78 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.21 Å2 / Biso mean: 16.526 Å2 / Biso min: 5.66 Å2
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Refinement step | Cycle: final / Resolution: 1.18→46.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.181→1.212 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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