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Open data
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Basic information
Entry | Database: PDB / ID: 5fpu | ||||||
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Title | Crystal structure of human JARID1B in complex with GSKJ1 | ||||||
![]() | LYSINE-SPECIFIC DEMETHYLASE 5B | ||||||
![]() | TRANSCRIPTION / LYSINE-SPECIFIC DEMETHYLASE 5B | ||||||
Function / homology | ![]() 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 / transcription corepressor activity / sequence-specific double-stranded DNA binding / rhythmic process / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Srikannathasan, V. / Nowak, R. / Johansson, C. / Gileadi, C. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
![]() | ![]() Title: Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, ...Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, A. / Steuber, H. / Egner, U. / Badock, V. / Munro, S. / Lathangue, N.B. / Westaway, S. / Brown, J. / Athanasou, N. / Prinjha, R. / Brennan, P.E. / Oppermann, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.9 KB | Display | ![]() |
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PDB format | ![]() | 170.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798.7 KB | Display | ![]() |
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Full document | ![]() | 800.2 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uf0C ![]() 5a1fSC ![]() 5a3pC ![]() 5a3tC ![]() 5a3wC ![]() 5fpvC ![]() 5funC ![]() 5fupC ![]() 5fv3C ![]() 5fwjC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 55457.578 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 26-772 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 257 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/K0I.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K0I.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-K0I / | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EPE / | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | GGGG -GLYCINE LINKER NOT VISIBLE IN THE STRUCTURE -1 SER AND RESIDUE 0-MET FROM THE CONSTRUCT |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.12 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.1M HEPES PH 8.0, 0.8M POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2015 / Details: MIRRORS |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→95.46 Å / Num. obs: 43823 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 20.2 % / Biso Wilson estimate: 36.91 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.24→2.3 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 24.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5A1F Resolution: 2.24→64.601 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 21.49 / 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: 2.24→64.601 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 76.28 Å / Origin y: 65.9081 Å / Origin z: 11.2897 Å
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Refinement TLS group | Selection details: ALL |