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

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Basic information

Entry
Database: PDB / ID: 8ebh
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAATGGGG)
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*GP*CP*GP*GP*AP*AP*TP*GP*GP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*CP*CP*AP*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 / transcription regulator complex / sequence-specific DNA binding / 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: 1.33 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
DepositionAug 31, 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*GP*CP*GP*GP*AP*AP*TP*GP*GP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*CP*CP*AP*TP*TP*CP*CP*GP*CP*TP*TP*AP*T)-3')
F: Transcription factor PU.1


Theoretical massNumber of molelcules
Total (without water)22,2333
Polymers22,2333
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-23 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.939, 61.519, 44.394
Angle α, β, γ (deg.)90.000, 116.913, 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*TP*GP*GP*GP*G)-3')


Mass: 5036.292 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*GP*CP*TP*TP*AP*T)-3')


Mass: 4760.091 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.: 294 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
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: Mar 16, 2021
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→33.29 Å / Num. obs: 46513 / % possible obs: 98.15 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.97 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.04257 / Rpim(I) all: 0.02516 / Rrim(I) all: 0.04969 / Net I/σ(I): 16.72
Reflection shellResolution: 1.33→1.378 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4458 / Mean I/σ(I) obs: 3.37 / Num. unique obs: 4680 / CC1/2: 0.896 / CC star: 0.972 / Rpim(I) all: 0.2707 / Rrim(I) all: 0.5246 / % possible all: 99.4

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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: 1.33→33.29 Å / SU ML: 0.1385 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.2747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1739 1973 4.25 %
Rwork0.1387 44459 -
obs0.1402 46432 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.75 Å2
Refinement stepCycle: LAST / Resolution: 1.33→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 634 0 294 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791485
X-RAY DIFFRACTIONf_angle_d1.07282124
X-RAY DIFFRACTIONf_chiral_restr0.0661227
X-RAY DIFFRACTIONf_plane_restr0.0114157
X-RAY DIFFRACTIONf_dihedral_angle_d24.0976605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.26821340.24363199X-RAY DIFFRACTION99.43
1.36-1.40.21241350.20633188X-RAY DIFFRACTION99.19
1.4-1.440.2011560.1693194X-RAY DIFFRACTION98.59
1.44-1.490.18271360.14343001X-RAY DIFFRACTION93.22
1.49-1.540.18961250.14183158X-RAY DIFFRACTION98.29
1.54-1.60.16981470.13543194X-RAY DIFFRACTION99.64
1.6-1.680.17411530.1363202X-RAY DIFFRACTION99.08
1.68-1.760.21211500.13033213X-RAY DIFFRACTION99.2
1.76-1.870.1651420.12683191X-RAY DIFFRACTION98.96
1.87-2.020.17681260.13923120X-RAY DIFFRACTION96.21
2.02-2.220.17331430.14243174X-RAY DIFFRACTION98.6
2.22-2.540.17411420.13213244X-RAY DIFFRACTION99.44
2.54-3.20.19011510.14213184X-RAY DIFFRACTION98
3.2-33.290.14721330.13023197X-RAY DIFFRACTION96.47

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