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- PDB-6wx8: SOX2 bound to Importin-alpha 3 -

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Basic information

Entry
Database: PDB / ID: 6wx8
TitleSOX2 bound to Importin-alpha 3
Components
  • Importin subunit alpha-3
  • Transcription factor SOX-2
KeywordsNUCLEAR PROTEIN
Function / homology
Function and homology information


glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / 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 ...glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / 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 / Specification of the neural plate border / pituitary gland development / positive regulation of cell-cell adhesion / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / Transcriptional Regulation by MECP2 / Transcriptional regulation of pluripotent stem cells / dopamine secretion / neuronal stem cell population maintenance / Germ layer formation at gastrulation / eye development / tissue regeneration / response to growth factor / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / miRNA binding / nuclear import signal receptor activity / negative regulation of neuron differentiation / forebrain development / inner ear development / somatic stem cell population maintenance / nuclear pore / Transcriptional and post-translational regulation of MITF-M expression and activity / male germ cell nucleus / Deactivation of the beta-catenin transactivating complex / positive regulation of cell differentiation / response to hydrogen peroxide / negative regulation of canonical Wnt signaling pathway / brain development / response to wounding / ISG15 antiviral mechanism / neuron differentiation / protein import into nucleus / osteoblast differentiation / 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 / gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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
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
Importin subunit alpha-3 / Transcription factor SOX-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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-3
B: Transcription factor SOX-2
C: Importin subunit alpha-3
D: Transcription factor SOX-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2229
Polymers122,7424
Non-polymers4805
Water4,089227
1
A: Importin subunit alpha-3
B: Transcription factor SOX-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6595
Polymers61,3712
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-46 kcal/mol
Surface area22640 Å2
MethodPISA
2
C: Importin subunit alpha-3
D: Transcription factor SOX-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5634
Polymers61,3712
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-35 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.580, 118.990, 94.870
Angle α, β, γ (deg.)90.000, 128.770, 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
Components on special symmetry positions
IDModelComponents
11A-780-

HOH

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Components

#1: Protein Importin subunit alpha-3 / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


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 Transcription factor SOX-2


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 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.2M (NH4)2SO4, 0.1M HEPES pH 6.5

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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: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.3→2.4 Å / Num. unique obs: 4570 / CC1/2: 0.323

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BW9

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
RfactorNum. reflection% reflection
Rfree0.245 2747 5.23 %
Rwork0.2202 49798 -
obs0.2215 52545 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7861 0 25 227 8113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00238031
X-RAY DIFFRACTIONf_angle_d0.494110923
X-RAY DIFFRACTIONf_chiral_restr0.03671272
X-RAY DIFFRACTIONf_plane_restr0.00391414
X-RAY DIFFRACTIONf_dihedral_angle_d15.30013007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.3697320.2971801X-RAY DIFFRACTION29.22
2.34-2.380.3011850.31381481X-RAY DIFFRACTION55.22
2.38-2.430.3244910.32541953X-RAY DIFFRACTION72.3
2.43-2.480.35311210.33372389X-RAY DIFFRACTION88.13
2.48-2.530.38341580.33292660X-RAY DIFFRACTION99.16
2.53-2.590.3311260.31512716X-RAY DIFFRACTION99.93
2.59-2.660.33431500.31252694X-RAY DIFFRACTION99.86
2.66-2.730.32551450.27932703X-RAY DIFFRACTION99.79
2.73-2.810.30341720.27212661X-RAY DIFFRACTION99.86
2.81-2.90.30111440.25382707X-RAY DIFFRACTION99.89
2.9-30.27841470.24752680X-RAY DIFFRACTION99.82
3-3.120.28551430.25232702X-RAY DIFFRACTION99.86
3.12-3.260.30811500.23652684X-RAY DIFFRACTION99.79
3.26-3.430.2721450.232707X-RAY DIFFRACTION99.69
3.43-3.650.23571480.21892701X-RAY DIFFRACTION99.86
3.65-3.930.21651580.18732693X-RAY DIFFRACTION99.82
3.93-4.330.19971420.17432729X-RAY DIFFRACTION99.72
4.33-4.950.20251500.18282695X-RAY DIFFRACTION99.79
4.95-6.230.24451730.21012698X-RAY DIFFRACTION99.83
6.23-29.750.17331670.17092744X-RAY DIFFRACTION99.49

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