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- PDB-5zfy: Crystal structure of human DUX4 homeodomains bound to A12C DNA mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zfy | ||||||
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Title | Crystal structure of human DUX4 homeodomains bound to A12C DNA mutant | ||||||
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![]() | TRANSCRIPTION/DNA / homeodomains / DUX4 / DNA recognition / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() negative regulation of G0 to G1 transition / Zygotic genome activation (ZGA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation ...negative regulation of G0 to G1 transition / Zygotic genome activation (ZGA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / apoptotic process / chromatin / nucleolus / regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, Y.Y. / Wu, B.X. / Gan, J.H. | ||||||
![]() | ![]() Title: Structural basis for multiple gene regulation by human DUX4. Authors: Li, Y. / Wu, B. / Liu, H. / Gao, Y. / Yang, C. / Chen, X. / Zhang, J. / Chen, Y. / Gu, Y. / Li, J. / Ma, J. / Gan, 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 | ![]() | 66.2 KB | Display | ![]() |
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PDB format | ![]() | 43.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.7 KB | Display | ![]() |
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Full document | ![]() | 431 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z6zSC ![]() 5zfwC ![]() 5zfzC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17386.805 Da / Num. of mol.: 1 / Fragment: double homeodomains Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 5638.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 6011.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.1 M Sodium malonate pH 4.0, 12% Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977776 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 17918 / % possible obs: 99.6 % / Redundancy: 12.3 % / Net I/σ(I): 22.95 |
Reflection shell | Resolution: 2.3→2.38 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5Z6Z Resolution: 2.3→29.941 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 20.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.941 Å
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Refine LS restraints |
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LS refinement shell |
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