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- PDB-6vge: Crystal structure of the DNA binding domains of human transcripti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vge | |||||||||
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Title | Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC | |||||||||
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![]() | TRANSCRIPTION / Ewing sarcoma / enhancer / transcription factor / oncogenesis / prostate cancer / ETS-family / Runt-family | |||||||||
Function / homology | ![]() ligamentous ossification / regulation of fibroblast growth factor receptor signaling pathway / RUNX3 regulates RUNX1-mediated transcription / osteoblast fate commitment / RUNX1 regulates transcription of genes involved in BCR signaling / regulation of odontogenesis of dentin-containing tooth / chondrocyte development / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex ...ligamentous ossification / regulation of fibroblast growth factor receptor signaling pathway / RUNX3 regulates RUNX1-mediated transcription / osteoblast fate commitment / RUNX1 regulates transcription of genes involved in BCR signaling / regulation of odontogenesis of dentin-containing tooth / chondrocyte development / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / bHLH transcription factor binding / lymphocyte differentiation / positive regulation of chondrocyte differentiation / response to sodium phosphate / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / YAP1- and WWTR1 (TAZ)-stimulated gene expression / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endochondral ossification / myeloid cell differentiation / SMAD protein signal transduction / RUNX3 Regulates Immune Response and Cell Migration / embryonic cranial skeleton morphogenesis / definitive hemopoiesis / embryonic forelimb morphogenesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / osteoblast development / smoothened signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / bone mineralization / positive regulation of stem cell proliferation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of cell differentiation / RUNX2 regulates osteoblast differentiation / odontogenesis of dentin-containing tooth / RUNX3 regulates p14-ARF / hemopoiesis / T cell differentiation / regulation of ossification / chondrocyte differentiation / BMP signaling pathway / positive regulation of osteoblast differentiation / negative regulation of smoothened signaling pathway / cell maturation / ossification / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / stem cell differentiation / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / neuron differentiation / chromatin DNA binding / Transcriptional regulation of granulopoiesis / osteoblast differentiation / protein polyubiquitination / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / protein phosphorylation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hou, C. / Tsodikov, O.V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins. Authors: Hou, C. / Mandal, A. / Rohr, J. / Tsodikov, O.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.5 KB | Display | ![]() |
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PDB format | ![]() | 152.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 252.8 KB | Display | ![]() |
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Full document | ![]() | 252.8 KB | Display | |
Data in XML | ![]() | 929 B | Display | |
Data in CIF | ![]() | 4.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vg2C ![]() 6vg8C ![]() 6vgdSC ![]() 6vggC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14927.827 Da / Num. of mol.: 1 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Details: The N-terminal GPHM is left over from the affinity tag after its cleavage Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 4954.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA / Source: (synth.) ![]() |
#3: DNA chain | Mass: 4843.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA / Source: (synth.) ![]() |
#4: Protein | Mass: 19542.148 Da / Num. of mol.: 1 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 18263.381 Da / Num. of mol.: 1 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Details: The N-terminal AGSSHHHHHHSQDP is the affinity tag. The gaps correspond to disorder in the crystal. Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.47 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.25→50 Å / Num. obs: 7550 / % possible obs: 94.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 4.25→4.32 Å / Rmerge(I) obs: 1.382 / Num. unique obs: 367 / CC1/2: 0.785 / CC star: 0.938 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6VGD Resolution: 4.25→35 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.907 / SU B: 240.05 / SU ML: 1.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.96 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 438.53 Å2 / Biso mean: 282.708 Å2 / Biso min: 189.17 Å2
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Refinement step | Cycle: final / Resolution: 4.25→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.25→4.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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