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- PDB-6wx9: SOX2 bound to Importin-alpha 5 -

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Basic information

Entry
Database: PDB / ID: 6wx9
TitleSOX2 bound to Importin-alpha 5
Components
  • Importin subunit alpha-5
  • Transcription factor SOX-2
KeywordsNUCLEAR 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 / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / Inhibition of nitric oxide production / response to oxygen-glucose deprivation / endodermal cell fate specification ...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 / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / Inhibition of nitric oxide production / response to oxygen-glucose deprivation / endodermal cell fate specification / adenohypophysis development / 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 / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / positive regulation of cell-cell adhesion / tissue regeneration / Transcriptional Regulation by MECP2 / Transcriptional regulation of pluripotent stem cells / eye development / neuronal stem cell population maintenance / Germ layer formation at gastrulation / Transport of Ribonucleoproteins into the Host Nucleus / response to growth factor / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / NLS-bearing protein import into nucleus / Apoptosis induced DNA fragmentation / nuclear localization sequence binding / regulation of canonical Wnt signaling pathway / miRNA binding / nuclear import signal receptor activity / Vpr-mediated nuclear import of PICs / Integration of provirus / inner ear development / somatic stem cell population maintenance / negative regulation of neuron differentiation / nuclear pore / forebrain development / Transcriptional and post-translational regulation of MITF-M expression and activity / Assembly of the ORC complex at the origin of replication / positive regulation of cell differentiation / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / brain development / ISG15 antiviral mechanism / response to wounding / neuron differentiation / protein import into nucleus / osteoblast differentiation / Interferon alpha/beta signaling / chromatin organization / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / postsynaptic density / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / dendrite / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / glutamatergic synapse / 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
Transcription factor SOX / SOX transcription factor / : / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. ...Transcription factor SOX / SOX transcription factor / : / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / HMG (high mobility group) box / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Transcription factor SOX-2 / Importin subunit alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBikshapathi, J. / Stewart, M. / Forwood, J.K. / Aragao, D. / Roman, N.
CitationJournal: 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
DepositionMay 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 29, 2023Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-5
B: Transcription factor SOX-2


Theoretical massNumber of molelcules
Total (without water)62,7712
Polymers62,7712
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-2 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.460, 61.420, 69.100
Angle α, β, γ (deg.)90.000, 95.490, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Importin subunit alpha-5 / Karyopherin subunit alpha-1 / Nucleoprotein interactor 1 / NPI-1 / RAG cohort protein 2 / SRP1-beta


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
#2: Protein Transcription factor SOX-2


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 / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium/potassium phosphate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.8→2.9 Å / Num. unique obs: 2377 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B18

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
RfactorNum. reflection% reflection
Rfree0.2506 626 4.88 %
Rwork0.2057 12215 -
obs0.2079 12841 77.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.27 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 0 36 3462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373483
X-RAY DIFFRACTIONf_angle_d0.6614724
X-RAY DIFFRACTIONf_chiral_restr0.2227558
X-RAY DIFFRACTIONf_plane_restr0.0041604
X-RAY DIFFRACTIONf_dihedral_angle_d14.54131299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.3274760.29271439X-RAY DIFFRACTION36.71
3.08-3.530.32031410.26772933X-RAY DIFFRACTION74.36
3.53-4.440.24952040.20153875X-RAY DIFFRACTION98.08
4.44-290.21362050.17413968X-RAY DIFFRACTION98.28

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