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Yorodumi- PDB-4ys3: Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acety... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ys3 | ||||||||||||
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Title | Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / dyad axis / STRUCTURAL PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||||||||
Authors | Dechassa, M.L. / Luger, K. / Chatterjee, N. / North, J.A. / Manohar, M. / Prasad, R. / Ottessen, J.J. / Poirier, M.G. / Bartholomew, B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Mol.Cell.Biol. / Year: 2015 Title: Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF. Authors: Chatterjee, N. / North, J.A. / Dechassa, M.L. / Manohar, M. / Prasad, R. / Luger, K. / Ottesen, J.J. / Poirier, M.G. / Bartholomew, B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ys3.cif.gz | 322.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ys3.ent.gz | 245.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ys3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/4ys3 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/4ys3 | HTTPS FTP |
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-Related structure data
Related structure data | 4xzqC 4z66C 1p3lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 11584.492 Da / Num. of mol.: 2 / Fragment: residues 39-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 8910.394 Da / Num. of mol.: 2 / Fragment: residues 25-103 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 11724.677 Da / Num. of mol.: 2 / Fragment: residues 15-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #4: Protein | Mass: 10376.928 Da / Num. of mol.: 2 / Fragment: residues 34-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45368.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#6: DNA chain | Mass: 45359.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 1 types, 53 molecules
#7: 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 | Density Matthews: 2.98 Å3/Da / Density % sol: 58.71 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: postassium chloride, manganese chloride, cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 2, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→47.54 Å / Num. obs: 42733 / % possible obs: 99.7 % / Redundancy: 6.78 % / Rmerge(I) obs: 0.115 / Χ2: 0.96 / Net I/σ(I): 8.8 / Num. measured all: 291877 / Scaling rejects: 2191 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P3L Resolution: 3→47.45 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Bsol: 28.4034 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 203.96 Å2 / Biso mean: 81.0162 Å2 / Biso min: 6.97 Å2
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Refinement step | Cycle: final / Resolution: 3→47.45 Å
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Refine LS restraints |
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Xplor file |
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