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Yorodumi- PDB-7xv8: Crystal structure of the Human TR4 DNA-Binding Domain Homodimer B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xv8 | ||||||
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Title | Crystal structure of the Human TR4 DNA-Binding Domain Homodimer Bound to DR1 Response Element | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Transcriptional regulation / DNA BINDING / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of embryonic development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / nervous system development / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation ...positive regulation of embryonic development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / nervous system development / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) DNA molecule (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.199 Å | ||||||
Authors | Liu, Y. / Chen, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Structures of human TR4LBD-JAZF1 and TR4DBD-DNA complexes reveal the molecular basis of transcriptional regulation. Authors: Liu, Y. / Ma, L. / Li, M. / Tian, Z. / Yang, M. / Wu, X. / Wang, X. / Shang, G. / Xie, M. / Chen, Y. / Liu, X. / Jiang, L. / Wu, W. / Xu, C. / Xia, L. / Li, G. / Dai, S. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xv8.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xv8.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xv8_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7xv8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7xv8_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7xv8_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/7xv8 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/7xv8 | HTTPS FTP |
-Related structure data
Related structure data | 7xv6C 7xv9C 7xvaC 3dzuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8861.415 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR2C2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P49116 #2: DNA chain | | Mass: 5614.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) #3: DNA chain | | Mass: 5418.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG4000, sodium citrate, ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.199→50 Å / Num. obs: 5486 / % possible obs: 90.1 % / Redundancy: 5.8 % / CC1/2: 0.984 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 3.199→3.28 Å / Num. unique obs: 4919 / CC1/2: 0.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DZU Resolution: 3.199→47.708 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.192 / SU B: 18.716 / SU ML: 0.325 / Average fsc free: 0.931 / Average fsc work: 0.9401 / Cross valid method: FREE R-VALUE / ESU R Free: 0.516 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.473 Å2
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Refinement step | Cycle: LAST / Resolution: 3.199→47.708 Å
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Refine LS restraints |
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LS refinement shell |
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