- 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
Title
Solution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2
Components
Transcription factor SOX-2
Keywords
TRANSCRIPTION / 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 / regulation of cysteine-type endopeptidase activity involved in apoptotic process / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / 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 ...glial cell fate commitment / regulation of myofibroblast cell apoptotic process / 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 / 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 / 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 / response to growth factor / miRNA binding / somatic stem cell population maintenance / inner ear development / negative regulation of neuron differentiation / forebrain development / Deactivation of the beta-catenin transactivating complex / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / neuron differentiation / brain development / response to wounding / osteoblast differentiation / negative regulation of epithelial cell proliferation / 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 / positive regulation of MAPK cascade / 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 / 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 / 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
Name: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
Refinement
Method: 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 constraints
NOE 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 representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20
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