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- PDB-3wtv: Crystal structure of the complex comprised of ETS1(V170G), RUNX1,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wtv | ||||||
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Title | Crystal structure of the complex comprised of ETS1(V170G), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA | ||||||
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![]() | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION / DNA-BINDING / METHYLATION / NUCLEUS / PHOSPHOPROTEIN / TRANSCRIPTION REGULATION / ISOPEPTIDE BOND / PROTO-ONCOGENE / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / regulation of hair follicle cell proliferation / Organic cation transport / positive regulation of progesterone secretion / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity ...RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / regulation of hair follicle cell proliferation / Organic cation transport / positive regulation of progesterone secretion / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / core-binding factor complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX3 expression and activity / positive regulation of CD8-positive, alpha-beta T cell differentiation / positive regulation of cell maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / PML body organization / neuron fate commitment / Estrogen-dependent gene expression / myeloid cell differentiation / myeloid progenitor cell differentiation / definitive hemopoiesis / regulation of T cell anergy / embryonic hemopoiesis / positive regulation of leukocyte adhesion to vascular endothelial cell / hair follicle morphogenesis / behavioral response to pain / regulation of cell differentiation / hemopoiesis / negative regulation of cell cycle / basement membrane / regulation of signal transduction / neuron development / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / chondrocyte differentiation / response to retinoic acid / cell maturation / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / ossification / transcription corepressor binding / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / liver development / skeletal system development / central nervous system development / cell motility / promoter-specific chromatin binding / neuron differentiation / Oncogene Induced Senescence / positive regulation of miRNA transcription / positive regulation of inflammatory response / osteoblast differentiation / protein polyubiquitination / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / positive regulation of type II interferon production / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / nucleic acid binding / transcription coactivator activity / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / response to antibiotic / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / 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 / protein-containing complex / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shiina, M. / Hamada, K. / Ogata, K. | ||||||
![]() | ![]() Title: A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions. Authors: Shiina, M. / Hamada, K. / Inoue-Bungo, T. / Shimamura, M. / Uchiyama, A. / Baba, S. / Sato, K. / Yamamoto, M. / Ogata, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.1 KB | Display | ![]() |
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Full document | ![]() | 528 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wtsSC ![]() 3wttC ![]() 3wtuC ![]() 3wtwC ![]() 3wtxC ![]() 3wtyC ![]() 3wtzC ![]() 3wu0C ![]() 3wu1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 3 types, 6 molecules AFBGCH
#1: Protein | Mass: 22871.711 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 60-263 / Mutation: L94K, V170G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 16684.729 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 19216.732 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 276-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 4 molecules DIEJ
#4: DNA chain | Mass: 4513.950 Da / Num. of mol.: 2 / Source method: obtained synthetically #5: DNA chain | Mass: 4665.032 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 1 types, 9 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 4% PEG 8000, 0.1M AMMONIUM ACETATE, 0.02M MAGNESIUM CHLORIDE, 0.05M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 42777 / % possible obs: 96.8 % / Redundancy: 9.6 % / Biso Wilson estimate: 63.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.413 / % possible all: 81.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3WTS Resolution: 2.7→45.26 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2477205.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.2294 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→45.26 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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