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Open data
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Basic information
Entry | Database: PDB / ID: 4qwn | ||||||
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Title | Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure | ||||||
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![]() | Oxidoreductase/Structural Protein / cupin subfamily Fe(II)/2-OG dioxygenase / JmjC domain / Histone demethylase / Oxidoreductase-Structural Protein complex | ||||||
Function / homology | ![]() Chromatin modifying enzymes / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / Interleukin-7 signaling / HDMs demethylate histones / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines ...Chromatin modifying enzymes / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / Interleukin-7 signaling / HDMs demethylate histones / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / neuroepithelial cell differentiation / Factors involved in megakaryocyte development and platelet production / unmethylated CpG binding / Estrogen-dependent gene expression / negative regulation of transcription by competitive promoter binding / histone H3K36 demethylase activity / heart looping / histone demethylase activity / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / neural tube closure / transcription coregulator activity / circadian regulation of gene expression / neuron differentiation / multicellular organism growth / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / chromatin organization / gene expression / in utero embryonic development / protein heterodimerization activity / negative regulation of gene expression / chromatin binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, Z.J. / Patel, D.J. | ||||||
![]() | ![]() Title: A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36. Authors: Cheng, Z. / Cheung, P. / Kuo, A.J. / Yukl, E.T. / Wilmot, C.M. / Gozani, O. / Patel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.8 KB | Display | ![]() |
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PDB format | ![]() | 145.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.1 KB | Display | ![]() |
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Full document | ![]() | 496.6 KB | Display | |
Data in XML | ![]() | 32.5 KB | Display | |
Data in CIF | ![]() | 45.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qx7C ![]() 4qx8C ![]() 4qxbC ![]() 4qxcC ![]() 4qxhC ![]() 4tn7C C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Lysine-specific demethylase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 39031.324 Da / Num. of mol.: 2 / Fragment: UNP residues 36-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: F6YRW4, UniProt: P59997*PLUS, [histone H3]-dimethyl-L-lysine36 demethylase #2: Protein | Mass: 7534.759 Da / Num. of mol.: 2 / Fragment: UNP residues 450-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: F6YRW4, UniProt: P59997*PLUS, [histone H3]-dimethyl-L-lysine36 demethylase |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 1652.940 Da / Num. of mol.: 2 / Fragment: UNP residues 30-44 / Source method: obtained synthetically / Details: mono-methylated H3 peptide was synthesized / Source: (synth.) ![]() ![]() |
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-Non-polymers , 3 types, 199 molecules ![](data/chem/img/AKG.gif)
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![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2 M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2010 |
Radiation | Monochromator: 0.97918 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→85.94 Å / Num. all: 48785 / Num. obs: 47906 / % possible obs: 98.2 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.108 / Rsym value: 0.105 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3122 / Rsym value: 0.372 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.463 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→85.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.099→2.154 Å / Total num. of bins used: 20
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