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Open data
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Basic information
Entry | Database: PDB / ID: 8bx1 | ||||||
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Title | Oct4/Sox2 protein:DNA complex | ||||||
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![]() | TRANSCRIPTION / Oct4 / Sox2 / Hoxb1 | ||||||
Function / homology | ![]() diencephalon morphogenesis / olfactory placode formation / lens induction in camera-type eye / ectodermal cell fate commitment / response to benzoic acid / retina morphogenesis in camera-type eye / regulation of myofibroblast cell apoptotic process / mesodermal cell fate commitment / HMG box domain binding / detection of mechanical stimulus involved in equilibrioception ...diencephalon morphogenesis / olfactory placode formation / lens induction in camera-type eye / ectodermal cell fate commitment / response to benzoic acid / retina morphogenesis in camera-type eye / regulation of myofibroblast cell apoptotic process / mesodermal cell fate commitment / HMG box domain binding / detection of mechanical stimulus involved in equilibrioception / pigment biosynthetic process / trophectodermal cell fate commitment / forebrain neuron differentiation / anatomical structure formation involved in morphogenesis / blastocyst growth / adenohypophysis development / positive regulation of epithelial cell differentiation / regulation of asymmetric cell division / response to oxygen-glucose deprivation / endodermal cell fate specification / Deactivation of the beta-catenin transactivating complex / endodermal cell fate commitment / germ-line stem cell population maintenance / positive regulation of cell-cell adhesion / POU domain binding / detection of mechanical stimulus involved in sensory perception of sound / negative regulation of calcium ion-dependent exocytosis / neuron fate commitment / trophectodermal cell differentiation / neuronal stem cell population maintenance / male genitalia development / female germ cell nucleus / cell fate specification / germ cell nucleus / tongue development / epithelial tube branching involved in lung morphogenesis / inner ear morphogenesis / stem cell population maintenance / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / positive regulation of neuroblast proliferation / lung alveolus development / negative regulation of Wnt signaling pathway / positive regulation of Notch signaling pathway / cytokine binding / somatic stem cell population maintenance / negative regulation of cell differentiation / blastocyst development / inner ear development / negative regulation of neuron differentiation / regulation of neurogenesis / neuroblast proliferation / positive regulation of transcription initiation by RNA polymerase II / negative regulation of osteoblast differentiation / cell fate commitment / embryonic organ development / cis-regulatory region sequence-specific DNA binding / response to retinoic acid / forebrain development / Notch signaling pathway / cellular response to cadmium ion / positive regulation of neuron differentiation / transcription repressor complex / : / cellular response to leukemia inhibitory factor / male germ cell nucleus / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / lysine-acetylated histone binding / negative regulation of canonical Wnt signaling pathway / neuron differentiation / brain development / chromatin DNA binding / cerebral cortex development / Wnt signaling pathway / osteoblast differentiation / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chojnowski, G. / Wilmanns, M. / Round, E. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of Oct4-Soc2-HoxB1 complex Authors: Chojnowski, G. / Wilmanns, M. / Round, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.6 KB | Display | ![]() |
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PDB format | ![]() | 110.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.9 KB | Display | ![]() |
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Full document | ![]() | 452.5 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ht5S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10092.858 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 6752.419 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: DNA chain | Mass: 6747.374 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 17962.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1M sodium acetate, 12% (v/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2021 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→126.92 Å / Num. obs: 15480 / % possible obs: 99.7 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 2 / Num. unique obs: 1711 / CC1/2: 0.755 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ht5 Resolution: 2.5→58.48 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.916 / SU B: 26.716 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.215 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→58.48 Å
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