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5 results for “JMJD1B”
Experimental data for PanDDA analysis of human JMJD1B
<p>The repository contains processed data from the entire crystallographic fragment screen of human JMJD1B at the XChem facility of Diamond Light Source beamline I04-1 (JMJD1BA_XChem_screen.tar.bz2). Additionally, metadata about the experiment can be found in the <em>mainTable</em> of the corresponding SQLite database file (JMJD1BA_XChem_screen.sqlite). All identified ligand-bound structures were deposited in the Protein Data Bank under Group ID <strong><a href="https://www.rcsb.org/search/structure?q=pdbx_deposit_group.group_id:G_1002146">G_1002146</a>. </strong>All structures necessary to reproduce the deposited PanDDA event maps which were used for ligand identification were deposited in the Protein Data Bank under PDB ID <a href="https://www.rcsb.org/structure/5R7X">5R7X</a> (group ID <strong><a href="https://www.rcsb.org/search/structure?q=pdbx_deposit_group.group_id:G_1002141">G_1002141</a></strong>).</p> <p> </p> <p><strong><em>Usage:</em></strong></p> <p>download <em>JMJD1BA_XChem_screen.tar.bz2</em> and save into the desired project directory, e.g.</p> <p><strong>/home/me/JMJD1B</strong></p> <p>unpack the tar archive:</p> <p><strong>tar –xvjf JMJD1BA_XChem_screen.tar.bz2</strong></p> <p>run pandda, e.g.</p> <p><strong>pandda.analyse data_dirs="/home/me/JMJD1B/*" out_dir="/home/me/JMJD1B_pandda" pdb_style=dimple.pdb mtz_style=dimple.mtz</strong></p> <p>For more information about PanDDA, please check the <a href="http://www.ccp4.ac.uk/html/pandda.html">PanDDA CCP4 program documentation</a>.</p> <p> </p> <p><strong><em>Reference:</em></strong></p> <p>Pearce, N. M. <em>et al.</em> A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. <em>Nature Communications</em> <strong>8</strong>, ncomms15123 (2017).</p> <p> </p>
Human Lysine Demethylase JMJD1B (KDM3B); A Target Enabling Package
<p>There are 3 members of the Lysine Demethylase JMJD1 (KDM3) family, JMJD1A-C. SGC Oxford has expressed, purified and crystallized the catalytic domains of JMJD1A, JMJD1B and JMJD1C as part of the probe programme. Fragment screening and X-ray crystallography identified a large number of binders, some of which were progressed into a medicinal chemistry programme. Despite significant effort molecules with probe properties were not obtained. Consequently it has been decided to put the information generated into the public domain.</p>
Define roles of JMJD1B in mediating histone demethylation and gene expression
GEO Series GSE94966. Mus musculus. 35 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
JMJD1B target gene screening :JMJD1B is the H3K9 demethylase involved in transcriptional activation of Lmo2 in leukemia
GEO Series GSE30294. Homo sapiens. 5 samples. Type: Expression profiling by array.
DNA microarray analysis of Jmjd1a and/or Jmjd1b knockout embryonic stem cells
GEO Series GSE98761. Mus musculus. 8 samples. Type: Expression profiling by array.
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