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- PDB-2le4: Solution structure of the HMG box DNA-binding domain of human ste... -

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Basic information

Entry
Database: PDB / ID: 2le4
TitleSolution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2
ComponentsTranscription factor SOX-2
KeywordsTRANSCRIPTION / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
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 / 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 / response to growth factor / miRNA binding / inner ear development / somatic stem cell population maintenance / negative regulation of neuron differentiation / forebrain development / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of cell differentiation / Deactivation of the beta-catenin transactivating complex / 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 / cytosol / cytoplasm
Similarity search - Function
Transcription factor SOX / SOX transcription factor / : / High mobility group box domain / DNA Binding (I), subunit A / 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 ...Transcription factor SOX / SOX transcription factor / : / High mobility group box domain / DNA Binding (I), subunit A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor SOX-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model 17
AuthorsSahu, S.C. / Markley, J.L. / Tonelli, M. / Bahrami, A. / Eghbalnia, H.R. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Solution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2
Authors: Sahu, S. / Markley, J. / Tonelli, M. / Bahrami, A. / Eghbalnia, H.
History
DepositionJun 6, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor SOX-2


Theoretical massNumber of molelcules
Total (without water)9,9211
Polymers9,9211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Transcription factor SOX-2


Mass: 9920.610 Da / Num. of mol.: 1 / Fragment: HMG box DNA binding residues 39-118
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: 0.7 mM [U-100% 13C; U-100% 15N] Sox2, 7 % DTT, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMSox2-1[U-100% 13C; U-100% 15N]1
7 %DTT-21
Sample conditionsIonic strength: 100 mM / pH: 6.7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Inova / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. STRUCTURES ARE ...Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. STRUCTURES ARE BASED ON A TOTAL OF 1766 NOE CONSTRAINTS ( 597 INTRA, 423 SEQUENTIAL, 224 MEDIUM and 522 LONG RANGE CONSTRAINTS) AND 197 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1183 / NOE intraresidue total count: 205 / NOE long range total count: 168 / NOE medium range total count: 458 / NOE sequential total count: 352
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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