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Yorodumi- PDB-5fy9: Crystal structure of the catalytic domain of human JARID1B in com... -
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-Basic information
Entry | Database: PDB / ID: 5fy9 | |||||||||
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Title | Crystal structure of the catalytic domain of human JARID1B in complex with pyruvate | |||||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B | |||||||||
Keywords | OXIDOREDUCTASE / JARID1B / PLU1 / TCA INTERMEDIATE | |||||||||
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 / histone demethylase activity / single fertilization / response to fungicide / Chromatin modifications during the maternal to zygotic transition (MZT) / post-embryonic development / cellular response to leukemia inhibitory factor / HDMs demethylate histones / rhythmic process / transcription corepressor activity / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / 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: 2.03 Å | |||||||||
Authors | Nowak, R. / Srikannathasan, V. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. ...Nowak, R. / Srikannathasan, V. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Pyruvate Authors: Nowak, R. / Srikannathasan, V. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / ...Authors: Nowak, R. / Srikannathasan, V. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fy9.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fy9.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fy9_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 5fy9_full_validation.pdf.gz | 471.5 KB | Display | |
Data in XML | 5fy9_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 5fy9_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/5fy9 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/5fy9 | HTTPS FTP |
-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 , 6 types, 244 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PYR / | #7: 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: 2.11 Å3/Da / Density % sol: 41.64 % / 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 / 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: 2.03→95.88 Å / Num. obs: 59276 / % possible obs: 100 % / Observed criterion σ(I): 18.3 / Redundancy: 19.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 19.4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A3P Resolution: 2.03→57.135 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 24.73 / Stereochemistry target values: ML
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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: 2.03→57.135 Å
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Refine LS restraints |
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LS refinement shell |
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