[English] 日本語
Yorodumi- PDB-6vgg: Crystal structure of the DNA binding domains of human transcripti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vgg | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC | |||||||||
Components |
| |||||||||
Keywords | TRANSCRIPTION / Ewing sarcoma / enhancer / transcription factor / oncogenesis / prostate cancer / ETS-family / Runt-family | |||||||||
Function / homology | Function and homology information 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) / RUNX2 regulates genes involved in cell migration / YAP1- and WWTR1 (TAZ)-stimulated gene expression / 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 / BMP signaling pathway / regulation of cell differentiation / bone mineralization / positive regulation of stem cell proliferation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / odontogenesis of dentin-containing tooth / RUNX3 regulates p14-ARF / cell maturation / hemopoiesis / T cell differentiation / regulation of ossification / chondrocyte differentiation / positive regulation of osteoblast differentiation / ossification / negative regulation of smoothened signaling pathway / positive regulation of epithelial cell proliferation / epithelial cell proliferation / stem cell proliferation / stem cell differentiation / Transcriptional regulation of granulopoiesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of RUNX3 expression and activity / neuron differentiation / chromatin DNA binding / 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 / transcription regulator complex / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-binding transcription factor activity / protein phosphorylation / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.31 Å | |||||||||
Authors | Hou, C. / Rohr, J. / 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 | 6vgg.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vgg.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/6vgg ftp://data.pdbj.org/pub/pdb/validation_reports/vg/6vgg | HTTPS FTP |
---|
-Related structure data
Related structure data | 6vg2C 6vg8C 6vgdC 6vgeSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 3 molecules ADG
#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 sequence is left over from the affinity tag after its cleavage. Source: (gene. exp.) Homo sapiens (human) / Gene: ERG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11308 |
---|---|
#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.) Homo sapiens (human) / Gene: RUNX2, AML3, CBFA1, OSF2, PEBP2A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13950 |
#5: Protein | Mass: 18263.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal sequence AGSSHHHHHHSQDP is the affinity tag. Source: (gene. exp.) Homo sapiens (human) / Gene: CBFB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13951 |
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4954.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA / Source: (synth.) Homo sapiens (human) |
---|---|
#3: DNA chain | Mass: 4843.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 3 types, 5 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.9 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.3 M K/Na Tartrate, 50 mM Hepes, pH 7.0, soaked in 1 mM mithramycin-Mg |
-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: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.3→50 Å / Num. obs: 7632 / % possible obs: 98.3 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 4.3→4.37 Å / Rmerge(I) obs: 0.871 / Num. unique obs: 348 / CC1/2: 0.934 / % possible all: 93.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VGE Resolution: 4.31→35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 163.205 / SU ML: 0.938 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.875 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: 471.04 Å2 / Biso mean: 287.314 Å2 / Biso min: 175.73 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.31→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4.31→4.415 Å / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|