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- PDB-7jk7: Crystal structure of Importin alpha 2 in complex with LSD1 NLS S1... -
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Basic information
Entry | Database: PDB / ID: 7jk7 | ||||||
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Title | Crystal structure of Importin alpha 2 in complex with LSD1 NLS S111E mutant | ||||||
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![]() | PROTEIN TRANSPORT / Importin alpha demethylase nuclear localisation | ||||||
Function / homology | ![]() guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Sensing of DNA Double Strand Breaks / demethylase activity / entry of viral genome into host nucleus through nuclear pore complex via importin / telomeric repeat-containing RNA binding / positive regulation of viral life cycle ...guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Sensing of DNA Double Strand Breaks / demethylase activity / entry of viral genome into host nucleus through nuclear pore complex via importin / telomeric repeat-containing RNA binding / positive regulation of viral life cycle / histone H3K4 demethylase activity / muscle cell development / NLS-dependent protein nuclear import complex / neuron maturation / positive regulation of neural precursor cell proliferation / postsynapse to nucleus signaling pathway / regulation of androgen receptor signaling pathway / MRF binding / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear import signal receptor activity / nuclear androgen receptor binding / nuclear localization sequence binding / regulation of double-strand break repair via homologous recombination / NLS-bearing protein import into nucleus / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cell size / histone demethylase activity / positive regulation of epithelial to mesenchymal transition / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / cytoplasmic stress granule / protein import into nucleus / regulation of protein localization / cellular response to UV / host cell / p53 binding / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / flavin adenine dinucleotide binding / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / oxidoreductase activity / transcription coactivator activity / postsynaptic density / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tu, W.J. / McCuaig, R. / Tan, A.H.Y. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstron, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. ...Tu, W.J. / McCuaig, R. / Tan, A.H.Y. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstron, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. / Tsimbalyuk, S. / Smith, K.M. / Yip, D. / Malik, L. / Prasana, T. / Milburn, P. / Rao, S. | ||||||
![]() | ![]() Title: Targeting Nuclear LSD1 to Reprogram Cancer Cells and Reinvigorate Exhausted T Cells via a Novel LSD1-EOMES Switch. Authors: Tu, W.J. / McCuaig, R.D. / Tan, A.H.Y. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J. / Tsimbalyuk, S. / Smith, K. / Yip, D. / Malik, L. / ...Authors: Tu, W.J. / McCuaig, R.D. / Tan, A.H.Y. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J. / Tsimbalyuk, S. / Smith, K. / Yip, D. / Malik, L. / Prasanna, T. / Milburn, P. / Rao, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.2 KB | Display | ![]() |
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PDB format | ![]() | 139.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jjmC ![]() 6bvtS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein/peptide | Mass: 3186.563 Da / Num. of mol.: 1 / Mutation: S111E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase | ||||
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#2: Protein | Mass: 50970.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9357 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.684 Å / Num. obs: 48384 / % possible obs: 96.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.96→1.96 Å / Rmerge(I) obs: 1.236 / Num. unique obs: 3645 / CC1/2: 0.583 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BVT Resolution: 1.96→41.684 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.9 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.14 Å2 / Biso mean: 52.9818 Å2 / Biso min: 25.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.96→41.684 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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