[English] 日本語
Yorodumi- PDB-6t78: Structure of human Sox11 transcription factor in complex with a s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t78 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human Sox11 transcription factor in complex with a short DNA fragment | ||||||||||||
Components |
| ||||||||||||
Keywords | NUCLEAR PROTEIN / Sox11 / transcription factor / pioneer factor / DNA | ||||||||||||
Function / homology | Function and homology information closure of optic fissure / positive regulation of lens epithelial cell proliferation / soft palate development / cornea development in camera-type eye / noradrenergic neuron differentiation / negative regulation of transcription regulatory region DNA binding / positive regulation of hippo signaling / negative regulation of lymphocyte proliferation / hard palate development / regulation of transforming growth factor beta receptor signaling pathway ...closure of optic fissure / positive regulation of lens epithelial cell proliferation / soft palate development / cornea development in camera-type eye / noradrenergic neuron differentiation / negative regulation of transcription regulatory region DNA binding / positive regulation of hippo signaling / negative regulation of lymphocyte proliferation / hard palate development / regulation of transforming growth factor beta receptor signaling pathway / lens morphogenesis in camera-type eye / embryonic skeletal system morphogenesis / embryonic digestive tract morphogenesis / neuroepithelial cell differentiation / camera-type eye morphogenesis / oligodendrocyte development / sympathetic nervous system development / eyelid development in camera-type eye / positive regulation of hormone secretion / positive regulation of BMP signaling pathway / positive regulation of ossification / positive regulation of neurogenesis / negative regulation of glial cell proliferation / ventricular septum morphogenesis / spinal cord development / lung morphogenesis / positive regulation of stem cell proliferation / outflow tract morphogenesis / skeletal muscle cell differentiation / glial cell proliferation / positive regulation of osteoblast differentiation / positive regulation of neuron differentiation / kidney development / brain development / neuron differentiation / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.504 Å | ||||||||||||
Authors | Dodonova, S.O. / Zhu, F. / Dienemann, C. / Taipale, J. / Cramer, P. | ||||||||||||
Funding support | Germany, 3items
| ||||||||||||
Citation | Journal: Nature / Year: 2020 Title: Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Authors: Svetlana O Dodonova / Fangjie Zhu / Christian Dienemann / Jussi Taipale / Patrick Cramer / Abstract: 'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions ...'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6t78.cif.gz | 137.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6t78.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 6t78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t78_validation.pdf.gz | 460.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6t78_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 6t78_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 6t78_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/6t78 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/6t78 | HTTPS FTP |
-Related structure data
Related structure data | 6t79C 6t7aC 6t7bC 6t7cC 6t7dC 1gt0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
#1: Protein | Mass: 12856.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOX11 / Plasmid: LIC-1B (MacroLabs) / Production host: Escherichia coli (E. coli) / References: UniProt: P35716 #2: DNA chain | Mass: 4890.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 4900.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Sodium Acetate 100 mM pH 4.5, Calcium Acetate Hydrate 200 mM, 15-18 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→45.956 Å / Num. obs: 17066 / % possible obs: 99.9 % / Redundancy: 20.55 % / Biso Wilson estimate: 75.835 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.129 / Χ2: 1.052 / Net I/σ(I): 16.54 / Num. measured all: 350700 / Scaling rejects: 96 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GT0 Resolution: 2.504→45.956 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.88
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 215.77 Å2 / Biso mean: 96.3747 Å2 / Biso min: 48.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.504→45.956 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 29.4328 Å / Origin y: 55.5287 Å / Origin z: 23.2924 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|