+Open data
-Basic information
Entry | Database: PDB / ID: 6bhd | ||||||
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Title | Crystal structure of SETDB1 with a modified H3 peptide | ||||||
Components |
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Keywords | TRANSFERASE / structural genomics / epigenetics / histone modification / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information [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 / Chromatin modifying enzymes / heterochromatin organization / 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 / Chromatin modifying enzymes / heterochromatin organization / 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 / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / methylation / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å | ||||||
Authors | Qin, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat Commun / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bhd.cif.gz | 123.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bhd.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 6bhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bhd_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 6bhd_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 6bhd_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6bhd_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/6bhd ftp://data.pdbj.org/pub/pdb/validation_reports/bh/6bhd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: SETDB1, KIAA0067, KMT1E / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2 References: UniProt: Q15047, histone-lysine N-methyltransferase | ||||
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#2: Protein/peptide | Mass: 1840.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431 | ||||
#3: Chemical | ChemComp-UNX / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9686 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2013 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→41.57 Å / Num. obs: 74273 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.059 / Net I/σ(I): 15.1 / Num. measured all: 274409 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: similar, nearly isomorphous crystal structure, to be published Resolution: 1.25→41.57 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.471 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Electron density suggests that a HEPES buffer molecule may bind in the aromatic cage of TD2. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
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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: 106.7 Å2 / Biso mean: 16.006 Å2 / Biso min: 6.74 Å2
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Refinement step | Cycle: final / Resolution: 1.25→41.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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