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- PDB-8iiy: Crystal structure of MBP fused GAS41 YEATS domain in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8iiy | ||||||
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Title | Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide | ||||||
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Function / homology | ![]() modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kikuchi, M. / Umehara, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: GAS41 promotes H2A.Z deposition through recognition of the N terminus of histone H3 by the YEATS domain. Authors: Kikuchi, M. / Takase, S. / Konuma, T. / Noritsugu, K. / Sekine, S. / Ikegami, T. / Ito, A. / Umehara, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.8 KB | Display | ![]() |
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PDB format | ![]() | 181.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7eifC ![]() 8iizC ![]() 8ij0C 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
#1: Protein | Mass: 57212.938 Da / Num. of mol.: 1 / Mutation: D108A, K109A, E198A, N199A, K265A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() Gene: YEATS4, GAS41 / Production host: ![]() ![]() ![]() | ||||||||
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#2: Protein/peptide | ![]() Mass: 2118.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Aug 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→50 Å / Num. obs: 35680 / % possible obs: 100 % / Redundancy: 11 % / Rsym value: 0.093 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.15→2.22 Å / Num. unique obs: 3067 / Rsym value: 1.433 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.24 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→45 Å
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Refine LS restraints |
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