+Open data
-Basic information
Entry | Database: PDB / ID: 2qqr | ||||||
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Title | JMJD2A hybrid tudor domains | ||||||
Components | JmjC domain-containing histone demethylation protein 3A | ||||||
Keywords | OXIDOREDUCTASE / HISTONE LYSINE DEMETHYLASE / TANDEM HYBRID TUDOR DOMAINS / METAL BINDING PROTEIN / Chromatin regulator / Dioxygenase / Host-virus interaction / Iron / Metal-binding / Nucleus / Phosphorylation / Polymorphism / Transcription / Transcription regulation / Zinc / Zinc-finger | ||||||
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: 1.8 Å | ||||||
Authors | Lee, J. / Botuyan, M.V. / Mer, G. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor. Authors: Lee, J. / Thompson, J.R. / Botuyan, M.V. / Mer, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qqr.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qqr.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qqr_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 2qqr_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 2qqr_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2qqr_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/2qqr ftp://data.pdbj.org/pub/pdb/validation_reports/qq/2qqr | HTTPS FTP |
-Related structure data
Related structure data | 2qqsC 2gfaS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13549.607 Da / Num. of mol.: 2 / Fragment: HYBRID TUDOR DOMAINS (Residues: 897-1011) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD2A, JHDM3A, JMJD2, KIAA0677 / Plasmid: pTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 #2: Chemical | ChemComp-SO4 / #3: 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: 3.72 Å3/Da / Density % sol: 66.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 35286 / % possible obs: 100 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 57.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GFA Resolution: 1.8→35.87 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.105 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.682 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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