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Yorodumi- PDB-2qqs: JMJD2A tandem tudor domains in complex with a trimethylated histo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qqs | ||||||
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Title | JMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20 peptide | ||||||
Components |
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Keywords | OXIDOREDUCTASE / HISTONE LYSINE DEMETHYLASE / METAL BINDING PROTEIN / PROTEIN-METHYLATED PEPTIDE COMPLEX / 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 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / methylated histone binding / Meiotic synapsis / telomere organization / positive regulation of neuron differentiation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / negative regulation of autophagy / response to nutrient levels / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / fibrillar center / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / protein-containing complex / DNA binding / RNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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 | 2qqs.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qqs.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qqs_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 2qqs_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 2qqs_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2qqs_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/2qqs ftp://data.pdbj.org/pub/pdb/validation_reports/qq/2qqs | HTTPS FTP |
-Related structure data
Related structure data | 2qqrSC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological unit is made of one molecule of JMJD2A and one molecule of methylated histone H4. |
-Components
#1: Protein | Mass: 13455.816 Da / Num. of mol.: 2 / Fragment: JMJD2A 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: Protein/peptide | Mass: 1369.662 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthetic methyalted histone H4 peptide derived from human sequence. References: UniProt: P62805*PLUS #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: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 293 K / Details: 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→50 Å / Num. obs: 5184 / % possible obs: 88.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.82→2.92 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 1.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QQR Resolution: 2.82→25.97 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.824 / SU B: 16.388 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / 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: 23.236 Å2
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Refinement step | Cycle: LAST / Resolution: 2.82→25.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→2.889 Å / Total num. of bins used: 20
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