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- PDB-1eaq: The RUNX1 Runt domain at 1.25A resolution: A structural switch an... -
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Basic information
Entry | Database: PDB / ID: 1eaq | ||||||
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Title | The RUNX1 Runt domain at 1.25A resolution: A structural switch and specifically bound chloride ions modulate DNA binding | ||||||
![]() | RUNT-RELATED TRANSCRIPTION FACTOR 1 | ||||||
![]() | TRANSCRIPTION/DNA / ACUTE MYELOID LEUKEMIA / AML / RUNX1 / RUNT DOMAIN / CHLORIDE BINDING / TRANSCRIPTION FACTOR / IG FOLD / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() 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 ...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 / positive regulation of cell maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / neuron fate commitment / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / definitive hemopoiesis / regulation of T cell anergy / embryonic hemopoiesis / hair follicle morphogenesis / regulation of cell differentiation / behavioral response to pain / hemopoiesis / basement membrane / regulation of signal transduction / neuron development / chondrocyte differentiation / response to retinoic acid / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / ossification / liver development / skeletal system development / central nervous system development / promoter-specific chromatin binding / neuron differentiation / positive regulation of type II interferon production / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / in utero embryonic development / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / 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 / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Backstrom, S. / Wolf-Watz, M. / Grundstrom, C. / Hard, T. / Grundstrom, T. / Sauer, U.H. | ||||||
![]() | ![]() Title: The Runx1 Runt Domain at 1.25 A Resolution: A Structural Switch and Specifically Bound Chloride Ions Modulate DNA Binding Authors: Backstrom, S. / Wolf-Watz, M. / Grundstrom, C. / Hard, T. / Grundstrom, T. / Sauer, U.H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
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PDB format | ![]() | 99.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.756045, -0.282533, -0.590399), Vector: |
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Components
#1: Protein | Mass: 15664.235 Da / Num. of mol.: 2 / Fragment: RUNT DOMAIN RESIDUES 36-185 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATION CYS 72 SER, CYS 81 SER / Source: (gene. exp.) ![]() ![]() Description: SE-MET LABELLED, REFOLDED FROM INCLUSION BODIES Plasmid: PET11C / Production host: ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Compound details | CHAIN A ENGINEERED MUTATION CYS 72 SER, CYS 81 SER CHAIN B ENGINEERED MUTATION CYS 72 SER, CYS 81 ...CHAIN A ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 34 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 Details: 25 % PEG 3350, 16% GLYCEROL, 130 MM NA CACODYLATE, PH 6.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 6, 1999 / Details: MIRROR | ||||||||||||
Radiation | Monochromator: SI(111), SI(113) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.25→37 Å / Num. obs: 71531 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 8.48 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3 | ||||||||||||
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2 / % possible all: 78 | ||||||||||||
Reflection | *PLUS Lowest resolution: 37 Å / Num. measured all: 606863 / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | *PLUS % possible obs: 78 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→25 Å
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Refine LS restraints |
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