+Open data
-Basic information
Entry | Database: PDB / ID: 6wx9 | ||||||
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Title | SOX2 bound to Importin-alpha 5 | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / Importin / SOX2 | ||||||
Function / homology | Function and homology information satellite cell activation involved in skeletal muscle regeneration / glial cell fate commitment / regulation of myofibroblast cell apoptotic process / skeletal muscle satellite cell proliferation / 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 / Inhibition of nitric oxide production / Formation of the anterior neural plate / adenohypophysis development ...satellite cell activation involved in skeletal muscle regeneration / glial cell fate commitment / regulation of myofibroblast cell apoptotic process / skeletal muscle satellite cell proliferation / 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 / Inhibition of nitric oxide production / Formation of the anterior neural plate / adenohypophysis development / response to oxygen-glucose deprivation / endodermal cell fate specification / negative regulation of cell cycle G1/S phase transition / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / regulation of DNA recombination / Specification of the neural plate border / pituitary gland development / positive regulation of cell-cell adhesion / Transcriptional Regulation by MECP2 / Transcriptional regulation of pluripotent stem cells / eye development / neuronal stem cell population maintenance / tissue regeneration / Germ layer formation at gastrulation / Transport of Ribonucleoproteins into the Host Nucleus / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / response to growth factor / Apoptosis induced DNA fragmentation / postsynapse to nucleus signaling pathway / regulation of canonical Wnt signaling pathway / miRNA binding / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Vpr-mediated nuclear import of PICs / Integration of provirus / somatic stem cell population maintenance / inner ear development / negative regulation of neuron differentiation / nuclear pore / forebrain development / Assembly of the ORC complex at the origin of replication / Deactivation of the beta-catenin transactivating complex / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / neuron differentiation / brain development / ISG15 antiviral mechanism / response to wounding / osteoblast differentiation / protein import into nucleus / negative regulation of epithelial cell proliferation / Interferon alpha/beta signaling / chromatin organization / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / transcription regulator complex / sequence-specific DNA binding / positive regulation of MAPK cascade / postsynaptic density / 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 / dendrite / regulation of DNA-templated transcription / chromatin / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 6wx9.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wx9.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wx9_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 6wx9_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 6wx9_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 6wx9_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/6wx9 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/6wx9 | HTTPS FTP |
-Related structure data
Related structure data | 6wx7C 6wx8C 4b18S 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: 51725.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA1, RCH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52294 |
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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: 2.7 Å3/Da / Density % sol: 54.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium/potassium phosphate, 20% (w/v) PEG3350 |
-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: Feb 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.1 Å / Num. obs: 16476 / % possible obs: 98.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 48.2 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 2377 / CC1/2: 0.813 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B18 Resolution: 2.8→29.05 Å / SU ML: 0.3284 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4571 / 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: 48.27 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→29.05 Å
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Refine LS restraints |
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LS refinement shell |
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