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- PDB-3n9n: ceKDM7A from C.elegans, complex with H3K4me3K9me2 peptide and NOG -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n9n | ||||||
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Title | ceKDM7A from C.elegans, complex with H3K4me3K9me2 peptide and NOG | ||||||
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![]() | OXIDOREDUCTASE / Histone / methylation / demethylase / PHD / JmjC / Fe(II) and alpha-KG (alpha-ketoglutarate)-dependent dioxygenase family | ||||||
Function / homology | ![]() PKMTs methylate histone lysines / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...PKMTs methylate histone lysines / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Condensation of Prophase Chromosomes / RMTs methylate histone arginines / histone H3K27me2/H3K27me3 demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding / transcription coregulator activity / structural constituent of chromatin / nucleosome / histone binding / protein heterodimerization activity / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, Y. / Hu, L. / Wang, P. / Hou, H. / Chen, C.D. / Xu, Y. | ||||||
![]() | ![]() Title: Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans Authors: Yang, Y. / Hu, L. / Wang, P. / Hou, H. / Lin, Y. / Liu, Y. / Li, Z. / Gong, R. / Feng, X. / Zhou, L. / Zhang, W. / Dong, Y. / Yang, H. / Lin, H. / Wang, Y. / Chen, C.D. / Xu, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.1 KB | Display | ![]() |
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PDB format | ![]() | 96.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.3 KB | Display | ![]() |
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Full document | ![]() | 483.6 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n9lC ![]() 3n9mSC ![]() 3n9oC ![]() 3n9pC ![]() 3n9qC C: citing same article ( S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 61945.496 Da / Num. of mol.: 1 / Fragment: PHD domain, UNP residues 201-724 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9GYI0, [histone H3]-dimethyl-L-lysine36 demethylase |
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#2: Protein/peptide | Mass: 3403.015 Da / Num. of mol.: 2 / Fragment: JMJC domain, UNP residues 2-33 / Source method: obtained synthetically / Details: chemical synthesis, purchased from a company / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 294 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/OGA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/OGA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FE2 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-OGA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% PEG 3350, 0.2M Sodium Fluoride, 0.1M Bis-Tris or HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 6, 2009 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2988→50 Å / Num. obs: 27466 / % possible obs: 100 % / Biso Wilson estimate: 38.19 Å2 / Num. measured all: 395510 |
Reflection shell | Resolution: 2.2988→2.38 Å / Redundancy: 14.4 % / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3N9M Resolution: 2.299→39.476 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.825 / SU ML: 0.34 / σ(F): 0.07 / Phase error: 24.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.943 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.28 Å2 / Biso mean: 46.1291 Å2 / Biso min: 16.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.299→39.476 Å
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Refine LS restraints |
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LS refinement shell |
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