+Open data
-Basic information
Entry | Database: PDB / ID: 8ekj | |||||||||||||||
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Title | Human PU.1 ETS-Domain (165-270) Bound to d(AATAAATGGAAGTGGG) | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / transcription factor / protein-DNA complex / ETS family / ETS / PU.1 / TRANSCRIPTION-DNA complex | |||||||||||||||
Function / homology | Function and homology information positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / positive regulation of microglial cell mediated cytotoxicity / myeloid leukocyte differentiation / TRAIL-activated apoptotic signaling pathway / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation ...positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / positive regulation of microglial cell mediated cytotoxicity / myeloid leukocyte differentiation / TRAIL-activated apoptotic signaling pathway / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation / defense response to tumor cell / regulation of DNA-binding transcription factor activity / negative regulation of non-canonical NF-kappaB signal transduction / oncogene-induced cell senescence / negative regulation of protein localization to chromatin / positive regulation of p38MAPK cascade / positive regulation of B cell differentiation / DNA-binding transcription repressor activity / STAT family protein binding / DNA-binding transcription activator activity / negative regulation of NF-kappaB transcription factor activity / interleukin-6-mediated signaling pathway / NFAT protein binding / cis-regulatory region sequence-specific DNA binding / transcription initiation-coupled chromatin remodeling / protein sequestering activity / regulation of erythrocyte differentiation / positive regulation of miRNA transcription / Transcriptional regulation of granulopoiesis / histone deacetylase binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / molecular adaptor activity / transcription cis-regulatory region binding / 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 gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | |||||||||||||||
Authors | Terrell, J.R. / Poon, G.M.K. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Cell Rep / Year: 2023 Title: DNA selection by the master transcription factor PU.1. Authors: Terrell, J.R. / Taylor, S.J. / Schneider, A.L. / Lu, Y. / Vernon, T.N. / Xhani, S. / Gumpper, R.H. / Luo, M. / Wilson, W.D. / Steidl, U. / Poon, G.M.K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ekj.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ekj.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ekj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/8ekj ftp://data.pdbj.org/pub/pdb/validation_reports/ek/8ekj | HTTPS FTP |
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-Related structure data
Related structure data | 8e3kSC 8e3rC 8e4hC 8e5yC 8ebhC 8ee9C 8ej6C 8ej8C 8ek3C 8ek8C 8ekuC 8ekvC 8ekzC 8em9C 8emdC 8engC 8eo1C 8eo4C 8eqgC 8eqkC 8eqlC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5035.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 4759.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 12436.583 Da / Num. of mol.: 1 / Fragment: ETS-Domain UNP residues 165-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPI1 / Production host: Escherichia coli (E. coli) / References: UniProt: P17947 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Sodium Acetate, 2% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2021 |
Radiation | Monochromator: Liquid nitrogen cooled dual crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→33.3 Å / Num. obs: 29862 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.27 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03946 / Rpim(I) all: 0.02359 / Rrim(I) all: 0.04616 / Net I/σ(I): 17.49 |
Reflection shell | Resolution: 1.54→1.595 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.05 / Num. unique obs: 2945 / CC1/2: 0.883 / CC star: 0.968 / Rpim(I) all: 0.2354 / Rrim(I) all: 0.4573 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8E3K Resolution: 1.54→33.3 Å / SU ML: 0.1549 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5819 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→33.3 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 6.29147929186 Å / Origin y: 1.06197461164 Å / Origin z: 4.98122736648 Å
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Refinement TLS group | Selection details: all |