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Open data
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Basic information
Entry | Database: PDB / ID: 6bhg | ||||||
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Title | Crystal structure of SETDB1 with a modified H3 peptide | ||||||
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Function / homology | ![]() [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / heterochromatin organization / Chromatin modifying enzymes / epigenetic regulation of gene expression ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / heterochromatin organization / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qin, S. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1. Authors: Jurkowska, R.Z. / Qin, S. / Kungulovski, G. / Tempel, W. / Liu, Y. / Bashtrykov, P. / Stiefelmaier, J. / Jurkowski, T.P. / Kudithipudi, S. / Weirich, S. / Tamas, R. / Wu, H. / Dombrovski, L. ...Authors: Jurkowska, R.Z. / Qin, S. / Kungulovski, G. / Tempel, W. / Liu, Y. / Bashtrykov, P. / Stiefelmaier, J. / Jurkowski, T.P. / Kudithipudi, S. / Weirich, S. / Tamas, R. / Wu, H. / Dombrovski, L. / Loppnau, P. / Reinhardt, R. / Min, J. / Jeltsch, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.6 KB | Display | ![]() |
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PDB format | ![]() | 90.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bhdC ![]() 6bheSC ![]() 6bhhC ![]() 6bhiC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 27670.734 Da / Num. of mol.: 1 / Fragment: UNP residues 190-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q15047, ![]() | ||
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#2: Protein/peptide | ![]() Mass: 1813.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
#3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 20% PEG5000 MME, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2013 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→41.56 Å / Num. obs: 53270 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.022 / Rrim(I) all: 0.042 / Net I/σ(I): 19.9 / Num. measured all: 196395 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: earlier version of coordinates of nearly isomorphous crystal structure (see PDB entry 6BHE) Resolution: 1.45→41.56 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.283 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: We thank Aiping Dong for collection of diffraction data. Water sites were picked with PHENIX. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. ...Details: We thank Aiping Dong for collection of diffraction data. Water sites were picked with PHENIX. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Uninterpreted density in the aromatic cage of Tudor domain three may have arisen from the K9 side chain of bound histone peptide or from the R384 side chain of SETDB1.
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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 max: 89.44 Å2 / Biso mean: 20.631 Å2 / Biso min: 10.08 Å2
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Refinement step | Cycle: final / Resolution: 1.45→41.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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