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- PDB-7jjl: Crystal structure of Importin Alpha 3 in complex with human LSD1 NLS -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jjl | ||||||
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Title | Crystal structure of Importin Alpha 3 in complex with human LSD1 NLS | ||||||
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![]() | PROTEIN TRANSPORT / demethylase Importin alpha | ||||||
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 / demethylase activity / dopamine secretion / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...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 / demethylase activity / dopamine secretion / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / neuron maturation / positive regulation of neural precursor cell proliferation / 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 / nuclear pore / 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 / ISG15 antiviral mechanism / cerebral cortex development / positive regulation of neuron projection development / protein import into nucleus / regulation of protein localization / cellular response to UV / p53 binding / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / gene expression / flavin adenine dinucleotide binding / nuclear membrane / 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 / negative regulation of DNA-templated transcription / 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, H.Y.A. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. ...Tu, W.J. / McCuaig, R. / Tan, H.Y.A. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. / Tsimbalyuk, S. / Smith, K. / 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 | ![]() | 95.4 KB | Display | ![]() |
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PDB format | ![]() | 70.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434 KB | Display | ![]() |
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Full document | ![]() | 440.2 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bvzS 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
#1: Protein | Mass: 51120.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3144.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.44 % |
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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: 2.6→33.31 Å / Num. obs: 19536 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 2.6→2.6 Å / Rmerge(I) obs: 0.493 / Num. unique obs: 2323 / CC1/2: 0.778 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BVZ Resolution: 2.6→33.31 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 0.009 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 185.69 Å2 / Biso mean: 66.286 Å2 / Biso min: 29.89 Å2
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Refinement step | Cycle: final / Resolution: 2.6→33.31 Å
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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