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- PDB-7xv6: Crystal structure of the Human TR4 DNA-Binding Domain with C-term... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xv6 | ||||||
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Title | Crystal structure of the Human TR4 DNA-Binding Domain with C-terminal extension (DBD-CTE) Homodimer Bound to DR1 Response Element | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Transcriptional regulation / DNA BINDING / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() sequence-specific DNA binding / DNA-binding transcription factor activity / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() DNA molecule (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Chen, Z. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.6 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xv8C ![]() 7xv9C ![]() 7xvaC ![]() 3dzuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: DNA chain | Mass: 5614.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) | ||||||
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#2: DNA chain | Mass: 5418.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) | ||||||
#3: Protein | Mass: 9735.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A7L2NB91 #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Tris, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.297→50 Å / Num. obs: 15386 / % possible obs: 96.3 % / Redundancy: 7.1 % / CC1/2: 0.998 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.297→2.36 Å / Num. unique obs: 12867 / CC1/2: 0.853 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DZU Resolution: 2.3→31.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.465 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.346 / ESU R Free: 0.22 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: 31.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→31.53 Å
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Refine LS restraints |
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