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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 / telomere organization / Chromatin modifying enzymes ...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 / telomere organization / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / 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 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / p53 binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / chromosome / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / Oxidative Stress Induced Senescence / response to ethanol / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / DNA damage response / positive regulation of DNA-templated transcription / nucleolus / 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
Summary document | 1o9s_validation.pdf.gz | 514.8 KB | Display | wwPDB validaton report |
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Full document | 1o9s_full_validation.pdf.gz | 526.5 KB | Display | |
Data in XML | 1o9s_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1o9s_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9s ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9s | HTTPS FTP |
-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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