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- PDB-8hfp: Crystal structure of the methyl-CpG-binding domain of SETDB2 in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hfp | ||||||
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Title | Crystal structure of the methyl-CpG-binding domain of SETDB2 in complex with the cysteine-rich domain of C11orf46 protein | ||||||
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![]() | TRANSCRIPTION / Complex / Zn-binding / Heterochromatin / Histone methylation | ||||||
Function / homology | ![]() : / positive regulation of DNA methylation-dependent heterochromatin formation / left/right axis specification / histone H3K9 methyltransferase activity / heart looping / heterochromatin organization / Transferases; Transferring one-carbon groups; Methyltransferases / chromosome segregation / PKMTs methylate histone lysines / chromosome ...: / positive regulation of DNA methylation-dependent heterochromatin formation / left/right axis specification / histone H3K9 methyltransferase activity / heart looping / heterochromatin organization / Transferases; Transferring one-carbon groups; Methyltransferases / chromosome segregation / PKMTs methylate histone lysines / chromosome / mitotic cell cycle / cell division / negative regulation of gene expression / intracellular membrane-bounded organelle / focal adhesion / negative regulation of DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mahana, Y. / Ariyoshi, M. / Shirakawa, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural evidence for protein-protein interaction between the non-canonical methyl-CpG-binding domain of SETDB proteins and C11orf46. Authors: Mahana, Y. / Ariyoshi, M. / Nozawa, R.S. / Shibata, S. / Nagao, K. / Obuse, C. / Shirakawa, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79 KB | Display | ![]() |
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PDB format | ![]() | 57.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.1 KB | Display | ![]() |
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Full document | ![]() | 469.2 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 8413.624 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 12569.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96T68, [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.0 M ammonium sulfate 0.1 M Bis-Tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→42.06 Å / Num. obs: 30318 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rrim(I) all: 0.098 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.82→1.86 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1709 / CC1/2: 0.812 / Rpim(I) all: 0.294 / Rrim(I) all: 0.898 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: in-house model (SAD-phased) Resolution: 1.82→42.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.808 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 34.278 Å2
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Refinement step | Cycle: 1 / Resolution: 1.82→42.06 Å
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Refine LS restraints |
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