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- PDB-3wtt: Crystal structure of the complex comprised of phosphorylated ETS1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wtt | ||||||
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Title | Crystal structure of the complex comprised of phosphorylated ETS1, RUNX1, CBFBETA, and the tcralpha gene enhancer DNA | ||||||
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![]() | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / 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 / positive regulation of CD8-positive, alpha-beta T cell differentiation / Regulation of RUNX3 expression and activity / 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 / positive regulation of leukocyte adhesion to vascular endothelial cell / embryonic hemopoiesis / hair follicle morphogenesis / regulation of cell differentiation / behavioral response to pain / cell maturation / hemopoiesis / negative regulation of cell cycle / basement membrane / regulation of signal transduction / positive regulation of blood vessel endothelial cell migration / neuron development / regulation of angiogenesis / chondrocyte differentiation / ossification / response to retinoic acid / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / transcription corepressor binding / positive regulation of erythrocyte differentiation / positive regulation of miRNA transcription / liver development / nuclear receptor coactivator activity / skeletal system development / central nervous system development / cell motility / promoter-specific chromatin binding / Oncogene Induced Senescence / neuron differentiation / positive regulation of inflammatory response / osteoblast differentiation / protein polyubiquitination / positive regulation of type II interferon production / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / regulation of apoptotic process / transcription coactivator activity / nucleic acid binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / immune response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / response to antibiotic / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / 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 | ![]() | 196.6 KB | Display | ![]() |
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PDB format | ![]() | 149.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wtsSC ![]() 3wtuC ![]() 3wtvC ![]() 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: 22913.791 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 60-263 / Mutation: L94K 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, 127 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: 2.86 Å3/Da / Density % sol: 57.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 10% PEG 4000, 0.25M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, pH 5.5, 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: May 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 64857 / % possible obs: 98.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.519 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3WTS Resolution: 2.35→48.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2354630 / 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: 53.18 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.49 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→48.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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