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Yorodumi- PDB-1o9s: Crystal structure of a ternary complex of the human histone methy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o9s | ||||||
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Title | Crystal structure of a ternary complex of the human histone methyltransferase SET7/9 | ||||||
Components |
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Keywords | TRANSFERASE / METHYLATION / HISTONE H3 / METHYLTRANSFERASE | ||||||
Function / homology | Function and homology information heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / 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 / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / p53 binding / gene expression / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Xiao, B. / Jing, C. / Wilson, J.R. / Walker, P.A. / Vasisht, N. / Kelly, G. / Howell, S. / Taylor, I.A. / Blackburn, G.M. / Gamblin, S.J. | ||||||
Citation | Journal: Nature / Year: 2003 Title: Structure and Catalytic Mechanism of the Human Histone Methyltransferase Set7/9 Authors: Xiao, B. / Jing, C. / Wilson, J.R. / Walker, P.A. / Vasisht, N. / Kelly, G. / Howell, S. / Taylor, I.A. / Blackburn, G.M. / Gamblin, S.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9s.cif.gz | 228 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9s.ent.gz | 179.3 KB | Display | PDB format |
PDBx/mmJSON format | 1o9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9s ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9s | HTTPS FTP |
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-Related structure data
Related structure data | 1h3iS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | THE DIMER IN THIS ENTRY IS FORMED BY THE COMPLEXOF CHAIN A WITH A PEPTIDE CHAIN K AND CHAIN B WITHPEPTIDE CHAIN L. CHAINS A AND B ARE MONOMERIC IN THEPHYSIOLOGICAL STATE. |
-Components
#1: Protein | Mass: 28912.133 Da / Num. of mol.: 2 / Fragment: N-DOMAIN, SET-DOMAIN, RESIDUES 108-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q8WTS6, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1239.447 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-11 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16776, UniProt: P68431*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | pH: 7.8 / Details: pH 7.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 54703 / % possible obs: 89.9 % / Redundancy: 22 % / Rsym value: 0.055 / Net I/σ(I): 47.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H3I Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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