+Open data
-Basic information
Entry | Database: PDB / ID: 6wx7 | ||||||
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Title | SOX2 bound to Importin-alpha 2 | ||||||
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 / Sensing of DNA Double Strand Breaks / eye development / entry of viral genome into host nucleus through nuclear pore complex via importin / tissue regeneration / neuronal stem cell population maintenance / Germ layer formation at gastrulation / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / response to growth factor / postsynapse to nucleus signaling pathway / host cell / 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 / forebrain development / Deactivation of the beta-catenin transactivating complex / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / osteoblast differentiation / response to wounding / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / negative regulation of epithelial cell proliferation / chromatin organization / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / postsynaptic density / 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 / glutamatergic synapse / 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 | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 6wx7.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wx7.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/6wx7 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/6wx7 | HTTPS FTP |
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-Related structure data
Related structure data | 6wx8C 6wx9C 3ul1S 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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Unit cell |
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-Components
#1: Protein | Mass: 55268.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293 |
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#2: Protein | Mass: 11045.027 Da / Num. of mol.: 1 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 750mM sodium citrate (pH7), 10 mM DTT |
-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: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.1 Å / Num. obs: 18955 / % possible obs: 96.4 % / Redundancy: 10.2 % / Biso Wilson estimate: 42.1 Å2 / CC1/2: 0.922 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique obs: 2235 / CC1/2: 0.779 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UL1 Resolution: 2.7→29.1 Å / SU ML: 0.2941 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6377 / 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: 47.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.1 Å
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Refine LS restraints |
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LS refinement shell |
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