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Yorodumi- PDB-6u81: Crystal Structure of the Double Homeodomain of DUX4 in Complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u81 | ||||||
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Title | Crystal Structure of the Double Homeodomain of DUX4 in Complex with a DNA aptamer | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DUX tandem homeodomains / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information 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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.34 Å | ||||||
Authors | Shi, K. / Aihara, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Faseb J. / Year: 2020 Title: DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD. Authors: Klingler, C. / Ashley, J. / Shi, K. / Stiefvater, A. / Kyba, M. / Sinnreich, M. / Aihara, H. / Kinter, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u81.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u81.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 6u81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/6u81 ftp://data.pdbj.org/pub/pdb/validation_reports/u8/6u81 | HTTPS FTP |
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-Related structure data
Related structure data | 6u82C 6e8cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15629.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUX4, DUX10 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9UBX2 | ||||
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#2: DNA chain | Mass: 5179.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#3: DNA chain | Mass: 6099.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Ethylene glycols, Glycerol, PEG4000, Imidazole, MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→54.01 Å / Num. obs: 12667 / % possible obs: 96.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.74 Å2 / CC1/2: 0.999 / Net I/av σ(I): 6.7 / Net I/σ(I): 0.083 |
Reflection shell | Resolution: 2.31→2.39 Å / Rmerge(I) obs: 1.7 / Num. unique obs: 1897 / CC1/2: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6E8C Resolution: 2.34→46.27 Å / SU ML: 0.2606 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8337 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 29.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→46.27 Å
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Refine LS restraints |
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LS refinement shell |
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