+Open data
-Basic information
Entry | Database: PDB / ID: 5fyc | |||||||||
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Title | Crystal structure of human JMJD2A in complex with succinate | |||||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 4A | |||||||||
Keywords | OXIDOREDUCTASE / JMJD2A / KDM4A / TCA INTERMEDIATE | |||||||||
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: 2.261 Å | |||||||||
Authors | Nowak, R. / Kopec, J. / Johansson, C. / Szykowska, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Jmjd2A in Complex with Succinate Authors: Nowak, R. / Kopec, J. / Johansson, C. / Szykowska, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fyc.cif.gz | 161.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fyc.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fyc_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 5fyc_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 5fyc_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 5fyc_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/5fyc ftp://data.pdbj.org/pub/pdb/validation_reports/fy/5fyc | HTTPS FTP |
-Related structure data
Related structure data | 5a7oS 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-354 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) 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 , 6 types, 321 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: 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: 2.7 Å3/Da / Density % sol: 54.48 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.1M BIS-TRIS PH 6.0 -- 0.15M AMMONIUM SULFATE -- 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→30.1 Å / Num. obs: 41359 / % possible obs: 99.1 % / Observed criterion σ(I): 1.8 / Redundancy: 6.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.26→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A7O Resolution: 2.261→30.102 Å / σ(F): 1.35 / Stereochemistry target values: ML Details: SOME RESIDUE SIDECHAINS ARE IN DUAL CONFORMATION. SOME RESIDUES DO NOT HAVE SIDECHAINS.
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Solvent computation | Shrinkage radii: 2 Å / VDW probe radii: 2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.261→30.102 Å
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LS refinement shell |
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