+Open data
-Basic information
Entry | Database: PDB / ID: 2ybk | ||||||
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Title | JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 4A | ||||||
Keywords | OXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / DOUBLE-STRANDED BETA HELIX / DSBH / FACIAL TRIAD / METAL BINDING PROTEIN / EPIGENETIC AND TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / HYDROXYLATION | ||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Chowdhury, R. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: EMBO Rep. / Year: 2011 Title: The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. Authors: Chowdhury, R. / Yeoh, K.K. / Tian, Y.M. / Hillringhaus, L. / Bagg, E.A. / Rose, N.R. / Leung, I.K. / Li, X.S. / Woon, E.C. / Yang, M. / McDonough, M.A. / King, O.N. / Clifton, I.J. / Klose, ...Authors: Chowdhury, R. / Yeoh, K.K. / Tian, Y.M. / Hillringhaus, L. / Bagg, E.A. / Rose, N.R. / Leung, I.K. / Li, X.S. / Woon, E.C. / Yang, M. / McDonough, M.A. / King, O.N. / Clifton, I.J. / Klose, R.J. / Claridge, T.D. / Ratcliffe, P.J. / Schofield, C.J. / Kawamura, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ybk.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ybk.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ybk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ybk_validation.pdf.gz | 463.9 KB | Display | wwPDB validaton report |
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Full document | 2ybk_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 2ybk_validation.xml.gz | 29 KB | Display | |
Data in CIF | 2ybk_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/2ybk ftp://data.pdbj.org/pub/pdb/validation_reports/yb/2ybk | HTTPS FTP |
-Related structure data
Related structure data | 2ybpC 2ybsC 2yc0C 2ydeC 2ox0S C: citing same article (ref.) 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 References: UniProt: O75164, 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 |
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-Non-polymers , 5 types, 196 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M CITRATE PH 5.5, 4MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.07 Å / Num. obs: 32359 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.74 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OX0 Resolution: 2.4→45.07 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 101857.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML Details: ALTHOUGH THE LIGAND, 2HG WAS MODELLED WITH FULL OCCUPANCY, ADDITIONAL POSITIVE DIFFERENCE DENSITY NEAR THE LIGAND BINDING SITE WAS SUGGESTIVE OF A POSSIBLE LOW OCCUPANCY ALTERNATE ...Details: ALTHOUGH THE LIGAND, 2HG WAS MODELLED WITH FULL OCCUPANCY, ADDITIONAL POSITIVE DIFFERENCE DENSITY NEAR THE LIGAND BINDING SITE WAS SUGGESTIVE OF A POSSIBLE LOW OCCUPANCY ALTERNATE CONFORMATION OR A BUFFER MOLECULE.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.756 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→45.07 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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