+Open data
-Basic information
Entry | Database: PDB / ID: 7xv9 | ||||||
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Title | Crystal structure of the Human TR4 DNA-Binding Domain | ||||||
Components | Nuclear receptor subfamily 2 group C member 2 | ||||||
Keywords | DNA BINDING PROTEIN / Nuclear receptor | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 | 7xv9.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xv9.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 7xv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xv9_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7xv9_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7xv9_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7xv9_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/7xv9 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/7xv9 | HTTPS FTP |
-Related structure data
Related structure data | 7xv6C 7xv8C 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: 9187.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR2C2, TAK1, TR4 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P49116 #2: Chemical | ChemComp-ZN / #3: 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: 1.81 Å3/Da / Density % sol: 32.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 31, 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: 1.599→50 Å / Num. obs: 17222 / % possible obs: 99.6 % / Redundancy: 9.1 % / CC1/2: 0.9957 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.599→1.64 Å / Num. unique obs: 15147 / CC1/2: 0.933 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DZU Resolution: 1.599→32.031 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.791 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.09 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: 16.573 Å2
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Refinement step | Cycle: LAST / Resolution: 1.599→32.031 Å
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Refine LS restraints |
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LS refinement shell |
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