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- PDB-9qpf: Solution structure of Sox2 DBD -

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Basic information

Entry
Database: PDB / ID: 9qpf
TitleSolution structure of Sox2 DBD
ComponentsTranscription factor SOX-2
KeywordsTRANSCRIPTION / HMG / DNA-binding / Pioneer Transcription factor
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 / neuronal stem cell population maintenance / Germ layer formation at gastrulation / eye development / tissue regeneration / response to growth factor / miRNA binding / negative regulation of neuron differentiation / forebrain development / inner ear development / somatic stem cell population maintenance / Transcriptional and post-translational regulation of MITF-M expression and activity / Deactivation of the beta-catenin transactivating complex / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / brain development / response to wounding / neuron differentiation / osteoblast differentiation / chromatin organization / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / 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 / 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 / : / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
Transcription factor SOX-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsOrsetti, A. / van Ingen, H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.M.21.138 Netherlands
CitationJournal: To Be Published
Title: Solution structure of Sox2 DBD reveals conformational Selection in DNA Binding
Authors: Orsetti, A. / Slejfer, J. / Ha, S. / Kevelam, D. / Tekkelenburg, J. / Schellevis, R. / Cojocaru, V. / van Ingen, H.
History
DepositionMar 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Transcription factor SOX-2


Theoretical massNumber of molelcules
Total (without water)11,7721
Polymers11,7721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, NOESYs, NMR Distance Restraints, 15N-RDCs
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1target function

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Components

#1: Protein Transcription factor SOX-2


Mass: 11771.786 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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic13D 1H-15N NOESY
131isotropic43D 1H-13C NOESY
143anisotropic32D 1H-15N HSQC
151isotropic22D 1H-15N HSQC
161isotropic33D HN(CA)CB

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.25 mM [U-13C; U-15N] Sox2-DBD, 135 mM potassium chloride, 20 mM TRIS, 15 mM sodium chloride, 0.01 % v/v sodium azide, 90% H2O/10% D2OSample 190% H2O/10% D2O
solution30.25 mM [U-13C; U-15N] Sox2-DBD, 135 mM potassium chloride, 20 mM TRIS, 15 mM sodium chloride, 0.01 % v/v sodium azide, 5 % v/v pentaethylene glycol monodecyl/n-Hexanol, 90% H2O/10% D2OSample 290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMSox2-DBD[U-13C; U-15N]1
135 mMpotassium chloridenatural abundance1
20 mMTRISnatural abundance1
15 mMsodium chloridenatural abundance1
0.01 % v/vsodium azidenatural abundance1
0.25 mMSox2-DBD[U-13C; U-15N]3
135 mMpotassium chloridenatural abundance3
20 mMTRISnatural abundance3
15 mMsodium chloridenatural abundance3
0.01 % v/vsodium azidenatural abundance3
5 % v/vpentaethylene glycol monodecyl/n-Hexanolnatural abundance3
Sample conditionsIonic strength: 150 mM / Label: Condition 1 / pH: 7.3 / Pressure: AMBIENT bar / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO12001
Bruker AVANCE NEOBrukerAVANCE NEO9002
Bruker AVANCE IIIBrukerAVANCE III6003
Bruker AVANCE IIIBrukerAVANCE III8504

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.15Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3.98.15Guntert, Mumenthaler and Wuthrichchemical shift assignment
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leechemical shift assignment
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leedata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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