[English] 日本語
Yorodumi- PDB-6vg8: Crystal structure of the DNA binding domains of human FLI1 and Ru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vg8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with 16-mer DNA CAGAGGATGTGGCTTC | |||||||||
Components |
| |||||||||
Keywords | TRANSCRIPTION / Oncogenesis / Ewing sarcoma / Enhancer / Bone cancer / Leukemia / ETS-family / Runt-family | |||||||||
Function / homology | Function and homology information ligamentous ossification / regulation of fibroblast growth factor receptor signaling pathway / osteoblast fate commitment / regulation of odontogenesis of dentin-containing tooth / chondrocyte development / RUNX2 regulates bone development / RUNX2 regulates chondrocyte maturation / bHLH transcription factor binding / positive regulation of chondrocyte differentiation / response to sodium phosphate ...ligamentous ossification / regulation of fibroblast growth factor receptor signaling pathway / osteoblast fate commitment / regulation of odontogenesis of dentin-containing tooth / chondrocyte development / RUNX2 regulates bone development / RUNX2 regulates chondrocyte maturation / bHLH transcription factor binding / positive regulation of chondrocyte differentiation / response to sodium phosphate / 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 / endochondral ossification / SMAD protein signal transduction / embryonic cranial skeleton morphogenesis / embryonic forelimb morphogenesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / blood circulation / osteoblast development / megakaryocyte development / smoothened signaling pathway / bone mineralization / positive regulation of stem cell proliferation / regulation of cell differentiation / RUNX2 regulates osteoblast differentiation / odontogenesis of dentin-containing tooth / 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 / neuron differentiation / chromatin DNA binding / osteoblast differentiation / Transcriptional regulation of granulopoiesis / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / 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 / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.31 Å | |||||||||
Authors | Hou, C. / Tsodikov, O.V. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Structure / Year: 2021 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vg8.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vg8.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vg8_validation.pdf.gz | 249.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vg8_full_validation.pdf.gz | 249.3 KB | Display | |
Data in XML | 6vg8_validation.xml.gz | 924 B | Display | |
Data in CIF | 6vg8_validation.cif.gz | 3.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/6vg8 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/6vg8 | HTTPS FTP |
-Related structure data
Related structure data | 6vg2C 6vgdC 6vgeC 6vggC 5jvtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
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 sequence is the remainder of an affinity tag after its cleavage and removal. Source: (gene. exp.) Homo sapiens (human) / Gene: FLI1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01543 |
---|---|
#2: DNA chain | Mass: 4954.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA oligomer / Source: (synth.) Homo sapiens (human) |
#3: DNA chain | Mass: 4843.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA oligomer / Source: (synth.) Homo sapiens (human) |
#4: Protein | Mass: 13701.669 Da / Num. of mol.: 1 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RUNX2, AML3, CBFA1, OSF2, PEBP2A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13950 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 7.22 Å3/Da / Density % sol: 82.95 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 7% w/v PEG 4000, 50 mM Na Citrate, pH 5.6, 4% v/v isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 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: 16635 / % possible obs: 93.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 3.25→3.31 Å / Rmerge(I) obs: 0.433 / Num. unique obs: 696 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JVT Resolution: 4.31→34.21 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.962 / SU B: 74.824 / SU ML: 0.835 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.709 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 410.55 Å2 / Biso mean: 246.997 Å2 / Biso min: 165.91 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.31→34.21 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4.31→4.418 Å / Rfactor Rfree error: 0
|