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- PDB-8eo4: Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAAGTGGG) with... -

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Basic information

Entry
Database: PDB / ID: 8eo4
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAAGTGGG) with Di-methylated CpG sites
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*AP*T)-3')
  • Transcription factor PU.1
KeywordsTRANSCRIPTION/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 / 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 activator activity / positive regulation of B cell differentiation / DNA-binding transcription repressor activity / negative regulation of NF-kappaB transcription factor activity / STAT family protein binding / interleukin-6-mediated signaling pathway / NFAT protein binding / cis-regulatory region sequence-specific DNA binding / protein sequestering activity / transcription initiation-coupled chromatin remodeling / 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 / sequence-specific DNA binding / transcription regulator complex / molecular adaptor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor PU.1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsTerrell, J.R. / Poon, G.M.K.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL155178 United States
National Science Foundation (NSF, United States)MCB2028902 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137160 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
CitationJournal: 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
DepositionOct 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*AP*AP*TP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*AP*T)-3')
F: Transcription factor PU.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2844
Polymers22,2613
Non-polymers231
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.905, 60.675, 44.538
Angle α, β, γ (deg.)90.000, 116.814, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: DNA chain DNA (5'-D(*AP*AP*TP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')


Mass: 5050.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*AP*T)-3')


Mass: 4774.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Transcription factor PU.1 / 31 kDa-transforming 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Sodium Acetate, pH=4.6, 2% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2021
RadiationMonochromator: Double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→33.25 Å / Num. obs: 56794 / % possible obs: 98.38 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.06 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.04157 / Rpim(I) all: 0.02559 / Rrim(I) all: 0.04911 / Net I/σ(I): 17.99
Reflection shellResolution: 1.24→1.284 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3564 / Mean I/σ(I) obs: 3.67 / Num. unique obs: 5672 / CC1/2: 0.939 / CC star: 0.984 / Rpim(I) all: 0.2135 / Rrim(I) all: 0.4179 / % possible all: 99.04

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8E3K

8e3k


Resolution: 1.24→33.25 Å / SU ML: 0.1102 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.0717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1651 1987 3.5 %
Rwork0.1374 54758 -
obs0.1384 56745 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.16 Å2
Refinement stepCycle: LAST / Resolution: 1.24→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 652 1 302 1724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991540
X-RAY DIFFRACTIONf_angle_d1.27932195
X-RAY DIFFRACTIONf_chiral_restr0.0752235
X-RAY DIFFRACTIONf_plane_restr0.0151167
X-RAY DIFFRACTIONf_dihedral_angle_d23.8187637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.270.21071530.17033877X-RAY DIFFRACTION98.75
1.27-1.310.19741500.15653941X-RAY DIFFRACTION99.61
1.31-1.340.18891440.14453948X-RAY DIFFRACTION99.61
1.34-1.390.20661340.1433948X-RAY DIFFRACTION99.46
1.39-1.440.17331440.13313929X-RAY DIFFRACTION98.74
1.44-1.490.17751250.12233679X-RAY DIFFRACTION93.63
1.49-1.560.12661530.10423947X-RAY DIFFRACTION99.73
1.56-1.640.13681380.1043967X-RAY DIFFRACTION99.52
1.64-1.750.15171330.10743943X-RAY DIFFRACTION99.17
1.75-1.880.12491380.11053942X-RAY DIFFRACTION99.13
1.88-2.070.14691460.12173785X-RAY DIFFRACTION94.91
2.07-2.370.17771440.13243960X-RAY DIFFRACTION99.81
2.37-2.990.14931470.15083962X-RAY DIFFRACTION98.82
2.99-33.250.18391380.1533930X-RAY DIFFRACTION96.6

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