+Open data
-Basic information
Entry | Database: PDB / ID: 6bhh | ||||||
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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 / mutant / 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 / FOURIER SYNTHESIS / Resolution: 1.85 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 | 6bhh.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bhh.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bhh_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 6bhh_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 6bhh_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6bhh_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/6bhh ftp://data.pdbj.org/pub/pdb/validation_reports/bh/6bhh | HTTPS FTP |
-Related structure data
Related structure data | 6bhdSC 6bheC 6bhgC 6bhiC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 27555.604 Da / Num. of mol.: 1 / Fragment: UNP residues 190-410 / Mutation: W358A 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 | #4: Chemical | ChemComp-UNX / #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: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 10, 2013 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.82→36.61 Å / Num. obs: 24394 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.074 / Rrim(I) all: 0.143 / Net I/σ(I): 7.9 / Num. measured all: 88658 / 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: earlier version of model from PDB entry 6BHD Resolution: 1.85→36.61 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.811 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.135 Details: PHENIX.REFINE was used for automated addition of solvent atoms to the model. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Note weak density for ...Details: PHENIX.REFINE was used for automated addition of solvent atoms to the model. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Note weak density for dimethyllysyl residues. Modeled sulfate ions may represent sulfonate moieties of partially disordered HEPES molecules.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.17 Å2 / Biso mean: 23.469 Å2 / Biso min: 11.06 Å2
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Refinement step | Cycle: final / Resolution: 1.85→36.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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