+Open data
-Basic information
Entry | Database: PDB / ID: 1gt0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a POU/HMG/DNA ternary complex | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / POU FACTORS / SOX PROTEINS | ||||||
Function / homology | Function and homology information diencephalon morphogenesis / olfactory placode formation / lens induction in camera-type eye / retina morphogenesis in camera-type eye / regulation of myofibroblast cell apoptotic process / detection of mechanical stimulus involved in equilibrioception / pigment biosynthetic process / forebrain neuron differentiation / anatomical structure formation involved in morphogenesis / adenohypophysis development ...diencephalon morphogenesis / olfactory placode formation / lens induction in camera-type eye / retina morphogenesis in camera-type eye / regulation of myofibroblast cell apoptotic process / detection of mechanical stimulus involved in equilibrioception / pigment biosynthetic process / forebrain neuron differentiation / anatomical structure formation involved in morphogenesis / adenohypophysis development / positive regulation of epithelial cell differentiation / response to oxygen-glucose deprivation / endodermal cell fate specification / Deactivation of the beta-catenin transactivating complex / negative regulation of cell cycle G1/S phase transition / positive regulation of cell-cell adhesion / detection of mechanical stimulus involved in sensory perception of sound / neuron fate commitment / trophectodermal cell differentiation / neuronal stem cell population maintenance / male genitalia development / RNA Polymerase III Transcription Initiation From Type 3 Promoter / response to growth factor / RNA Polymerase III Abortive And Retractive Initiation / cell fate specification / miRNA binding / tongue development / inner ear morphogenesis / epithelial tube branching involved in lung morphogenesis / stem cell population maintenance / positive regulation of neuroblast proliferation / negative regulation of Wnt signaling pathway / lung alveolus development / positive regulation of Notch signaling pathway / somatic stem cell population maintenance / negative regulation of cell differentiation / RNA polymerase II transcribes snRNA genes / negative regulation of neuron differentiation / regulation of neurogenesis / neuroblast proliferation / anatomical structure morphogenesis / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of osteoblast differentiation / cell fate commitment / embryonic organ development / response to retinoic acid / Notch signaling pathway / cellular response to cadmium ion / positive regulation of neuron differentiation / : / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / neuron differentiation / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / cerebral cortex development / Wnt signaling pathway / positive regulation of miRNA transcription / osteoblast differentiation / RNA polymerase II transcription regulator complex / negative regulation of epithelial cell proliferation / gene expression / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / positive regulation of MAPK cascade / cell differentiation / 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 / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Remenyi, A. / Wilmanns, M. | ||||||
Citation | Journal: Genes Dev. / Year: 2003 Title: Crystal Structure of a POU/Hmg/DNA Ternary Complex Suggests Differential Assembly of Oct4 and Sox2 on Two Enhancers Authors: Remenyi, A. / Lins, K. / Nissen, L.J. / Reinbold, R. / Scholer, H.R. / Wilmanns, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gt0.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gt0.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/1gt0 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/1gt0 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 7436.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FGF-4 ENHANCER / Source: (synth.) MUS MUSCULUS (house mouse) |
---|---|
#2: DNA chain | Mass: 7299.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FGF-4 ENHANCER / Source: (synth.) MUS MUSCULUS (house mouse) |
#3: Protein | Mass: 18327.795 Da / Num. of mol.: 1 / Fragment: POU DOMAIN RESIDUES 280-438 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14859 |
#4: Protein | Mass: 9833.532 Da / Num. of mol.: 1 / Fragment: HMG DOMAIN RESIDUES 41-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET24-D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48432 |
#5: Water | ChemComp-HOH / |
Compound details | CHAIN C ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % |
---|---|
Crystal grow | pH: 7 Details: 18% PEG3350, 50 MM HEPES PH 7.0, 20 MM MGCL2, 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.846 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.846 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 16619 / % possible obs: 98.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 80.3 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.35 / % possible all: 96.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.6→30 Å / Data cutoff high absF: 100000 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.66 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 16
|