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Open data
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Basic information
Entry | Database: PDB / ID: 8j0r | ||||||
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Title | Structure of human TFAP2A in complex with DNA | ||||||
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![]() | DNA BINDING PROTEIN/DNA / TFAP2 family / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() optic vesicle morphogenesis / optic cup structural organization / oculomotor nerve formation / positive regulation of tooth mineralization / nuclear receptor corepressor activity / trigeminal nerve development / TFAP2 (AP-2) family regulates transcription of other transcription factors / Specification of the neural plate border / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / retina layer formation ...optic vesicle morphogenesis / optic cup structural organization / oculomotor nerve formation / positive regulation of tooth mineralization / nuclear receptor corepressor activity / trigeminal nerve development / TFAP2 (AP-2) family regulates transcription of other transcription factors / Specification of the neural plate border / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / retina layer formation / TFAP2 (AP-2) family regulates transcription of cell cycle factors / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / negative regulation of transcription by competitive promoter binding / Activation of the TFAP2 (AP-2) family of transcription factors / embryonic cranial skeleton morphogenesis / embryonic forelimb morphogenesis / bone morphogenesis / inner ear morphogenesis / roof of mouth development / eyelid development in camera-type eye / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, K. / Xiao, Y.Q. / Li, W.F. / Min, J.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors. Authors: Liu, K. / Xiao, Y. / Gan, L. / Li, W. / Zhang, J. / Min, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.9 KB | Display | ![]() |
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PDB format | ![]() | 90.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8j0kC ![]() 8j0lC ![]() 8j0qC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23819.338 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 3912.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4032.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 368 molecules ![](data/chem/img/PG3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PG3 / | ||||||
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#5: Chemical | ChemComp-GOL / ![]() #6: Chemical | ![]() #7: Chemical | ![]() #8: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.62 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid (pH3.5), 34% PEG 200 (w/v). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→108.1 Å / Num. obs: 51127 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.998 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 4160 / CC1/2: 0.825 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.284 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→19.99 Å
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