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Yorodumi- PDB-5fz0: Crystal structure of the catalytic domain of human JARID1B in com... -
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-Basic information
Entry | Database: PDB / ID: 5fz0 | ||||||
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Title | Crystal structure of the catalytic domain of human JARID1B in complex with 2,5-dichloro-N-(pyridin-3-yl)thiophene-3-carboxamide (N08137b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 5B | ||||||
Keywords | OXIDOREUCTASE / JARID1B / PLU1 / PANDDA / FRAGMENT SOAKING / X-RAY FRAGMENT SCREENING | ||||||
Function / homology | Function and homology information regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus ...regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus / branching involved in mammary gland duct morphogenesis / single fertilization / histone demethylase activity / response to fungicide / cellular response to leukemia inhibitory factor / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / transcription corepressor activity / rhythmic process / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Nowak, R. / Krojer, T. / Pearce, N. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Burgess-Brown, N.A. / Arrowsmith, C.H. ...Nowak, R. / Krojer, T. / Pearce, N. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / von Delft, F. / Brennan, P.E. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N11213A Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / von Delft, ...Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / von Delft, F. / Brennan, P.E. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fz0.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fz0.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/5fz0 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/5fz0 | HTTPS FTP |
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-Related structure data
Related structure data | 5a3pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55214.297 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 26-101,374-770 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q9UGL1, 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 , 9 types, 108 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-EPE / | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-DJ6 / | #9: Chemical | ChemComp-PO4 / | #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES 102-373 WERE DELETED FROM THE ORIGINAL ...RESIDUES S AND M COME FROM THE EXPRESSION |
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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: 2.19 Å3/Da / Density % sol: 43.84 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92781 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92781 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→96.73 Å / Num. obs: 36349 / % possible obs: 100 % / Observed criterion σ(I): 1.3 / Redundancy: 19.9 % / Biso Wilson estimate: 56.57 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.42→2.48 Å / Redundancy: 21 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENRTY 5A3P Resolution: 2.42→96.735 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED. GLYCINE LINKER DOES NOT EXIST. LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED.
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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: 2.42→96.735 Å
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Refine LS restraints |
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LS refinement shell |
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