[English] 日本語
Yorodumi- PDB-8q9n: Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q9n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and MITR deacetylase binding motif mutant L151V. | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / transcriptional repressor | ||||||
Function / homology | Function and homology information animal organ development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein dimerization activity / 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: 1.51 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
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8q9n.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8q9n.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 8q9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q9n_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8q9n_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 8q9n_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 8q9n_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/8q9n ftp://data.pdbj.org/pub/pdb/validation_reports/q9/8q9n | HTTPS FTP |
-Related structure data
Related structure data | 8c84C 8pdeC 8q9pC 8q9qC 8q9rC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) |
---|---|
#3: DNA chain | Mass: 4268.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-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.) Homo sapiens (human) / Gene: MEF2D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05BX2 #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.) Homo sapiens (human) |
---|
-Non-polymers , 2 types, 150 molecules
#5: Chemical | ChemComp-DMS / |
---|---|
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.39 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→45.76 Å / SU B: 1.857 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||
Displacement parameters | Biso mean: 26.105 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→45.76 Å
|