+Open data
-Basic information
Entry | Database: PDB / ID: 6wx8 | ||||||
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Title | SOX2 bound to Importin-alpha 3 | ||||||
Components |
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Keywords | NUCLEAR PROTEIN | ||||||
Function / homology | Function and homology information glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / regulation of cysteine-type endopeptidase activity involved in apoptotic process / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / adenohypophysis development / response to oxygen-glucose deprivation / endodermal cell fate specification / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation ...glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / regulation of cysteine-type endopeptidase activity involved in apoptotic process / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / adenohypophysis development / response to oxygen-glucose deprivation / endodermal cell fate specification / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / negative regulation of cell cycle G1/S phase transition / pituitary gland development / Transcriptional Regulation by MECP2 / positive regulation of cell-cell adhesion / Transcriptional regulation of pluripotent stem cells / dopamine secretion / eye development / tissue regeneration / neuronal stem cell population maintenance / Germ layer formation at gastrulation / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / response to growth factor / miRNA binding / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / somatic stem cell population maintenance / inner ear development / negative regulation of neuron differentiation / anatomical structure morphogenesis / nuclear pore / forebrain development / Deactivation of the beta-catenin transactivating complex / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / ISG15 antiviral mechanism / osteoblast differentiation / response to wounding / protein import into nucleus / negative regulation of epithelial cell proliferation / gene expression / chromatin organization / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / transcription regulator complex / sequence-specific DNA binding / positive regulation of MAPK cascade / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Bikshapathi, J. / Stewart, M. / Forwood, J.K. / Aragao, D. / Roman, N. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for nuclear import selectivity of pioneer transcription factor SOX2. Authors: Jagga, B. / Edwards, M. / Pagin, M. / Wagstaff, K.M. / Aragao, D. / Roman, N. / Nanson, J.D. / Raidal, S.R. / Dominado, N. / Stewart, M. / Jans, D.A. / Hime, G.R. / Nicolis, S.K. / Basler, C.F. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wx8.cif.gz | 243.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wx8.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 6wx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/6wx8 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/6wx8 | HTTPS FTP |
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-Related structure data
Related structure data | 6wx7C 6wx9C 6bw9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 50325.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00629 #2: Protein | Mass: 11045.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOX2 / Production host: Escherichia coli (E. coli) / References: UniProt: P48431 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.66 Å3/Da / Density % sol: 53.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.2M (NH4)2SO4, 0.1M HEPES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.5 Å / Num. obs: 56880 / % possible obs: 99.6 % / Redundancy: 13 % / Biso Wilson estimate: 44.95 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.3→2.4 Å / Num. unique obs: 4570 / CC1/2: 0.323 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BW9 Resolution: 2.3→29.1 Å / SU ML: 0.3596 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.3691 / Stereochemistry target values: CDL v1.2
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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 mean: 62.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.1 Å
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Refine LS restraints |
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LS refinement shell |
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