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- PDB-8ee9: Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAATGGGG) -

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Basic information

Entry
Database: PDB / ID: 8ee9
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAATGGGG)
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*TP*GP*GP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*CP*CP*AP*TP*TP*CP*CP*TP*TP*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 / positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / pro-T cell differentiation / negative regulation of neutrophil degranulation / follicular B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / germinal center B cell differentiation ...positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / pro-T cell differentiation / negative regulation of neutrophil degranulation / follicular B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / germinal center B cell differentiation / TRAIL-activated apoptotic signaling pathway / granulocyte differentiation / negative regulation of MHC class II biosynthetic process / endothelial to hematopoietic transition / negative regulation of adipose tissue development / apoptotic process involved in blood vessel morphogenesis / pericyte cell differentiation / immature B cell differentiation / myeloid dendritic cell differentiation / defense response to tumor cell / positive regulation of p38MAPK cascade / oncogene-induced cell senescence / negative regulation of non-canonical NF-kappaB signal transduction / negative regulation of protein localization to chromatin / 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 / NFAT protein binding / cellular response to ethanol / macrophage differentiation / somatic stem cell population maintenance / cis-regulatory region sequence-specific DNA binding / negative regulation of canonical NF-kappaB signal transduction / transforming growth factor beta receptor signaling pathway / transcription initiation-coupled chromatin remodeling / protein sequestering activity / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / erythrocyte differentiation / regulation of erythrocyte differentiation / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / 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 / regulation of transcription by RNA polymerase II / chromatin / 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: 1.22 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
DepositionSep 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,2313
Polymers22,2313
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-25 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.873, 61.185, 44.590
Angle α, β, γ (deg.)90.000, 117.160, 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*AP*AP*GP*GP*AP*AP*TP*GP*GP*GP*G)-3')


Mass: 5044.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*CP*CP*CP*AP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')


Mass: 4750.089 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2% PEG 3350, 100 mM Sodium Acetate, pH 4.6

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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: Feb 2, 2021
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→33.29 Å / Num. obs: 59154 / % possible obs: 96.88 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.03986 / Rpim(I) all: 0.02504 / Rrim(I) all: 0.04735 / Net I/σ(I): 18.56
Reflection shellResolution: 1.22→1.264 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3852 / Mean I/σ(I) obs: 4.18 / Num. unique obs: 5594 / CC1/2: 0.917 / CC star: 0.978 / Rpim(I) all: 0.2433 / Rrim(I) all: 0.4584 / % possible all: 92.4

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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: 1.22→33.29 Å / SU ML: 0.0891 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.19
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1561 1997 3.38 %
Rwork0.1441 57011 -
obs0.1445 59008 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.37 Å2
Refinement stepCycle: LAST / Resolution: 1.22→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 634 0 257 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00981485
X-RAY DIFFRACTIONf_angle_d1.23782124
X-RAY DIFFRACTIONf_chiral_restr0.0752227
X-RAY DIFFRACTIONf_plane_restr0.0153157
X-RAY DIFFRACTIONf_dihedral_angle_d24.3979605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.21161280.18153738X-RAY DIFFRACTION89.7
1.25-1.280.18131370.15924154X-RAY DIFFRACTION98.96
1.28-1.320.17041520.14524139X-RAY DIFFRACTION99.05
1.32-1.360.15091360.14584136X-RAY DIFFRACTION98.66
1.36-1.410.15041580.13944099X-RAY DIFFRACTION97.86
1.41-1.470.13411330.12734053X-RAY DIFFRACTION96.47
1.47-1.540.13411430.12074098X-RAY DIFFRACTION97.52
1.54-1.620.1541320.1164174X-RAY DIFFRACTION99.56
1.62-1.720.13621560.11434139X-RAY DIFFRACTION98.19
1.72-1.850.14621420.12754110X-RAY DIFFRACTION97.88
1.85-2.040.1411380.1373979X-RAY DIFFRACTION94.73
2.04-2.330.14331480.13964132X-RAY DIFFRACTION97.99
2.33-2.940.17821540.15984089X-RAY DIFFRACTION97.27
2.94-33.290.15881400.15153971X-RAY DIFFRACTION92.57

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