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Yorodumi- PDB-5zfz: Crystal structure of human DUX4 homeodomains bound to A12T DNA mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zfz | ||||||
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Title | Crystal structure of human DUX4 homeodomains bound to A12T DNA mutant | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / homeodomains / DUX4 / DNA recognition / TRANSCRIPTION-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 / 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 | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Li, Y.Y. / Wu, B.X. / Gan, J.H. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zfz.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zfz.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/5zfz ftp://data.pdbj.org/pub/pdb/validation_reports/zf/5zfz | HTTPS FTP |
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-Related structure data
Related structure data | 5z6zSC 5zfwC 5zfyC 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: 17386.805 Da / Num. of mol.: 1 / Fragment: double homeodomains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUX4L4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CJ87, UniProt: Q9UBX2*PLUS |
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#2: DNA chain | Mass: 5653.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 5995.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977776 Å |
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: 1.9→30 Å / Num. obs: 29905 / % possible obs: 98.7 % / Redundancy: 12.6 % / Net I/σ(I): 39.64 |
Reflection shell | Resolution: 1.9→1.97 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Z6Z Resolution: 1.9→29.877 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 21.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.877 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -37.7334 Å / Origin y: 14.5991 Å / Origin z: 164.5078 Å
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Refinement TLS group | Selection details: all |