+
Open data
-
Basic information
Entry | Database: PDB / ID: 8ekz | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGGAGAAGTAGG) | |||||||||||||||
![]() |
| |||||||||||||||
![]() | TRANSCRIPTION/DNA / transcription factor / protein-DNA complex / ETS family / ETS / PU.1 / TRANSCRIPTION-DNA complex | |||||||||||||||
Function / homology | ![]() positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / 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 / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / 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 / oncogene-induced cell senescence / negative regulation of non-canonical NF-kappaB signal transduction / negative regulation of protein localization to chromatin / positive regulation of p38MAPK cascade / DNA-binding transcription repressor activity / positive regulation of B cell differentiation / DNA-binding transcription activator activity / STAT family protein binding / interleukin-6-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / 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 / histone deacetylase binding / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / 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 / regulation of DNA-templated transcription / chromatin / 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 | ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Terrell, J.R. / Poon, G.M.K. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 140.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 88.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 422.4 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e3kSC ![]() 8e3rC ![]() 8e4hC ![]() 8e5yC ![]() 8ebhC ![]() 8ee9C ![]() 8ej6C ![]() 8ej8C ![]() 8ek3C ![]() 8ek8C ![]() 8ekjC ![]() 8ekuC ![]() 8ekvC ![]() 8em9C ![]() 8emdC ![]() 8engC ![]() 8eo1C ![]() 8eo4C ![]() 8eqgC ![]() 8eqkC ![]() 8eqlC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 5044.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 4750.089 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.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Sodium Acetate, pH=4.6, 2% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2022 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→23.01 Å / Num. obs: 36849 / % possible obs: 94.54 % / Redundancy: 4.1 % / Biso Wilson estimate: 17.24 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.03456 / Rpim(I) all: 0.02012 / Rrim(I) all: 0.04013 / Net I/σ(I): 22.83 |
Reflection shell | Resolution: 1.42→1.471 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.2969 / Mean I/σ(I) obs: 4.74 / Num. unique obs: 3684 / CC1/2: 0.963 / CC star: 0.991 / Rpim(I) all: 0.1652 / Rrim(I) all: 0.3403 / % possible all: 94.77 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8E3K Resolution: 1.42→23.01 Å / SU ML: 0.0907 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.4212 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→23.01 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|