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Yorodumi- PDB-4v2w: JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v2w | |||||||||
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Title | JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35) | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / JMJD2A / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / DOUBLE-STRANDED BETA HELIX / DSBH / FACIAL TRIAD / DEMETHYLASE / HISTONE / JMJC DOMAIN / 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 / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / pericentric heterochromatin / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Meiotic synapsis / Inhibition of DNA recombination at telomere / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / negative regulation of autophagy / Condensation of Prophase Chromosomes / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / Nonhomologous End-Joining (NHEJ) / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / G2/M DNA damage checkpoint / fibrillar center / structural constituent of chromatin / nucleosome / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / regulation of gene expression / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / DNA binding / zinc ion binding / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | |||||||||
Authors | Chowdhury, R. / Zafred, D. / Schofield, C.J. | |||||||||
Citation | Journal: Epigenetics / Year: 2014 Title: Studies on the Catalytic Domains of Multiple Jmjc Oxygenases Using Peptide Substrates. Authors: Williams, S.T. / Walport, L.J. / Hopkinson, R.J. / Madden, S.K. / Chowdhury, R. / 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 | 4v2w.cif.gz | 446.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v2w.ent.gz | 374.3 KB | Display | PDB format |
PDBx/mmJSON format | 4v2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v2w_validation.pdf.gz | 477.6 KB | Display | wwPDB validaton report |
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Full document | 4v2w_full_validation.pdf.gz | 482.5 KB | Display | |
Data in XML | 4v2w_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 4v2w_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/4v2w ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2w | HTTPS FTP |
-Related structure data
Related structure data | 4v2vC 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN UNP 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 #2: Protein/peptide | | Mass: 2055.447 Da / Num. of mol.: 1 / Fragment: HISTONE H3K27ME3 PEPTIDE, RESIDUES 17-36 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q16695 |
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-Non-polymers , 6 types, 509 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: 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: 2.64 Å3/Da / Density % sol: 53.5 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: VAPOUR DIFFUSION, SITTING DROP (PROTEIN:WELL, 1:2), 277 K, PACT PREMIER/G10: 0.02 M SODIUM/POTASSIUM PHOSPHATE, 0.1 M BIS TRIS PROPANE 7.5, 20 % W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→60.07 Å / Num. obs: 79999 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 31.89 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.81→1.91 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENRTY 2OX0 Resolution: 1.81→60.072 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 21.85 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→60.072 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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