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Yorodumi- PDB-8q9q: Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q9q | ||||||
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Title | Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC7 deacetylase binding motif | ||||||
Components |
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Keywords | TRANSCRIPTION / transcriptional repressor | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) DNA molecule (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Chinellato, M. / Carli, A. / Perin, S. / Mazzocato, Y. / Biondi, B. / Di Giorgio, E. / Brancolini, C. / Angelini, A. / Cendron, L. | ||||||
Funding support | Italy, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q9q.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q9q.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 8q9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q9q_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 8q9q_full_validation.pdf.gz | 459.2 KB | Display | |
Data in XML | 8q9q_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 8q9q_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/8q9q ftp://data.pdbj.org/pub/pdb/validation_reports/q9/8q9q | HTTPS FTP |
-Related structure data
Related structure data | 8c84C 8pdeC 8q9nC 8q9pC 8q9rC 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/peptide | Mass: 1685.101 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) | ||||||
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#2: 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.) Homo sapiens (human) / Gene: MEF2D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05BX2 #3: DNA chain | | Mass: 4286.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others) #4: DNA chain | | Mass: 4268.813 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others) #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 mM sodium acetate trihydrate, 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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→76.5 Å / Num. obs: 14910 / % possible obs: 96 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.11→2.17 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.732 / Num. unique obs: 1222 / CC1/2: 0.882 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→46.94 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.563 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.23 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→46.94 Å
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