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Yorodumi- PDB-1ljm: DNA recognition is mediated by conformational transition and by D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ljm | ||||||
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Title | DNA recognition is mediated by conformational transition and by DNA bending | ||||||
Components | RUNX1 transcription factor | ||||||
Keywords | TRANSCRIPTION / immunoglobulin fold / beta-sandwich | ||||||
Function / homology | Function and homology information regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX1 regulates transcription of genes involved in BCR signaling / Organic cation transport / RUNX1 regulates transcription of genes involved in interleukin signaling / myeloid leukocyte differentiation / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation ...regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX1 regulates transcription of genes involved in BCR signaling / Organic cation transport / RUNX1 regulates transcription of genes involved in interleukin signaling / myeloid leukocyte differentiation / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / regulation of cardiac muscle cell proliferation / cardiac muscle tissue regeneration / negative regulation of granulocyte differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of extracellular matrix organization / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of plasminogen activation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / hematopoietic stem cell proliferation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of cell differentiation / hemopoiesis / RUNX3 regulates p14-ARF / positive regulation of collagen biosynthetic process / chondrocyte differentiation / positive regulation of interleukin-2 production / ossification / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / neuron differentiation / Pre-NOTCH Transcription and Translation / transcription coactivator binding / Transcriptional regulation of granulopoiesis / positive regulation of angiogenesis / SARS-CoV-1 activates/modulates innate immune responses / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / calcium ion binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bartfeld, D. / Shimon, L. / Couture, G.C. / Rabinovich, D. / Frolow, F. / Levanon, D. / Groner, Y. / Shakked, Z. | ||||||
Citation | Journal: Structure Title: DNA Recognition by the RUNX1 Transcription Factor Is Mediated by an Allosteric Transition in the RUNT Domain and by DNA Bending. Authors: Bartfeld, D. / Shimon, L. / Couture, G. / Rabinovich, D. / Frolow, F. / Levanon, D. / Groner, Y. / Shakked, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ljm.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ljm.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ljm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/1ljm ftp://data.pdbj.org/pub/pdb/validation_reports/lj/1ljm | HTTPS FTP |
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-Related structure data
Related structure data | 1e50S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14579.675 Da / Num. of mol.: 2 / Fragment: Runt domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: human / Plasmid: RUNT-PV-8 / Production host: Escherichia coli (E. coli) / Strain (production host): PHS2 / References: UniProt: Q01196 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.76 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ethanol, Sodium Chloride, Tris-HCl, Hepes, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 18, 2000 / Details: mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43 Å / Num. all: 17501 / Num. obs: 17379 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.295 / % possible all: 99.3 |
Reflection | *PLUS Num. all: 17379 / Num. obs: 15686 / Num. measured all: 243124 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.295 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E50 Resolution: 2.5→43 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.5 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→43 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 43 Å / % reflection Rfree: 5 % / Rfactor obs: 0.1947 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.193 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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