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Yorodumi- PDB-8pde: Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pde | ||||||
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Title | Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC4 deacetylase binding motif | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Myocyte enhancer factor 2 / Class II Histone deacetylase | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 8pde.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pde.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 8pde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pde_validation.pdf.gz | 490.1 KB | Display | wwPDB validaton report |
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Full document | 8pde_full_validation.pdf.gz | 500.4 KB | Display | |
Data in XML | 8pde_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 8pde_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/8pde ftp://data.pdbj.org/pub/pdb/validation_reports/pd/8pde | HTTPS FTP |
-Related structure data
Related structure data | 8c84C 8q9nC 8q9pC 8q9qC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11254.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Missing residues are not traceable in the electron density maps Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05BX2 #2: Protein/peptide | Mass: 1939.322 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: synthetic peptide: missing residues are not traceable in the electron density maps Source: (synth.) Homo sapiens (human) #3: DNA chain | Mass: 4286.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: DNA chain | Mass: 4268.813 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
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 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 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: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.65 Å / Num. obs: 17911 / % possible obs: 94.7 % / Redundancy: 4.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.132 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1938 / CC1/2: 0.533 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.65 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.4→45.65 Å
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