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- PDB-8q9n: Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q9n | ||||||
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Title | Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and MITR deacetylase binding motif mutant L151V. | ||||||
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![]() | TRANSCRIPTION / transcriptional repressor | ||||||
Function / homology | ![]() histone deacetylase binding / heart development / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chinellato, M. / Carli, A. / Perin, S. / Mazzocato, Y. / Biondi, B. / Di Giorgio, E. / Brancolini, C. / Angelini, A. / Cendron, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA. Authors: Chinellato, M. / Perin, S. / Carli, A. / Lastella, L. / Biondi, B. / Borsato, G. / Di Giorgio, E. / Brancolini, C. / Cendron, L. / Angelini, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.1 KB | Display | ![]() |
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PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.4 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c84C ![]() 8pdeC ![]() 8q9pC ![]() 8q9qC ![]() 8q9rC 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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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules KL
#2: DNA chain | Mass: 4286.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 4268.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Protein / Protein/peptide , 2 types, 3 molecules ABX
#1: Protein | Mass: 11254.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Missing residues are not visible in the electron density maps Source: (gene. exp.) ![]() ![]() ![]() #4: Protein/peptide | | Mass: 2079.375 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Missing residues are not visible in the electron density maps Source: (synth.) ![]() |
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-Non-polymers , 2 types, 150 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-DMS / |
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#6: 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: 1.79 Å3/Da / Density % sol: 31.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 mM sodium formate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v polyethylene glycol 3350 (PEG 3350) |
-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: Nov 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→45.8 Å / Num. obs: 36328 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1562 / CC1/2: 0.752 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 26.105 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→45.76 Å
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