[English] 日本語
![](img/lk-miru.gif)
- PDB-6vgd: Crystal structure of the DNA binding domain (DBD) of human FLI1 a... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vgd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC | |||||||||
![]() |
| |||||||||
![]() | 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) / hemostasis / 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 / blood circulation / Regulation of RUNX1 Expression and Activity / osteoblast development / megakaryocyte 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 / animal organ morphogenesis / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / neuron differentiation / chromatin DNA binding / osteoblast differentiation / Transcriptional regulation of granulopoiesis / 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 / nuclear body / 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 / protein domain specific binding / 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 / 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 | ![]()
| |||||||||
![]() | ![]() Title: Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins. Authors: Hou, C. / Mandal, A. / Rohr, J. / Tsodikov, O.V. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 196.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 153.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 251.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 251.8 KB | Display | |
Data in XML | ![]() | 928 B | Display | |
Data in CIF | ![]() | 4.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vg2C ![]() 6vg8SC ![]() 6vgeC ![]() 6vggC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12098.655 Da / Num. of mol.: 1 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Details: The N-terminal GPHM is left from the affinity tag after its cleavage. Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#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 Source method: isolated from a genetically manipulated source Details: The N-terminal region AGSSHHHHHHSQDP is a cloned affinity tag. Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.26 Å3/Da / Density % sol: 71.1 % |
---|---|
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 |
---|---|
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: 3.25→50 Å / Num. obs: 17612 / % possible obs: 99.3 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3.25→3.31 Å / Rmerge(I) obs: 0.954 / Num. unique obs: 825 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6VG8 Resolution: 4.2→35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.949 / SU B: 187.362 / SU ML: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.823 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 466.18 Å2 / Biso mean: 285.539 Å2 / Biso min: 167.33 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.2→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4.2→4.307 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|