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- PDB-8eqg: Human PU.1 ETS-Domain (165-270) Bound to d(AATAAA(DU)GGAAGTGGG) -

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Basic information

Entry
Database: PDB / ID: 8eqg
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAA(DU)GGAAGTGGG)
Components
  • DNA (5'-D(*AP*AP*DU*AP*AP*AP*TP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*AP*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 / 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: 1.39 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 7, 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*DU*AP*AP*AP*TP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*AP*TP*TP*TP*AP*T)-3')
F: Transcription factor PU.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2404
Polymers22,2173
Non-polymers231
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-31 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.967, 60.278, 44.782
Angle α, β, γ (deg.)90.000, 116.337, 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*DU*AP*AP*AP*TP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')


Mass: 5021.277 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*AP*TP*TP*TP*AP*T)-3')


Mass: 4759.104 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.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Sodium Acetate, pH=4.6, 2% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2022
RadiationMonochromator: Vertical DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.39→24.1 Å / Num. obs: 41005 / % possible obs: 99.35 % / Redundancy: 5.2 % / Biso Wilson estimate: 18.69 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.07182 / Rpim(I) all: 0.03535 / Rrim(I) all: 0.08027 / Net I/σ(I): 11.96
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.5477 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 4053 / CC1/2: 0.88 / CC star: 0.968 / Rpim(I) all: 0.27447 / Rrim(I) all: 0.6144 / % possible all: 98.66

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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: 1.39→24.1 Å / SU ML: 0.1446 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1844 1992 4.86 %
Rwork0.1455 38970 -
obs0.1474 40962 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.47 Å2
Refinement stepCycle: LAST / Resolution: 1.39→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 633 1 281 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941482
X-RAY DIFFRACTIONf_angle_d1.15892114
X-RAY DIFFRACTIONf_chiral_restr0.0719227
X-RAY DIFFRACTIONf_plane_restr0.014157
X-RAY DIFFRACTIONf_dihedral_angle_d23.8986607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.29111300.23812733X-RAY DIFFRACTION98.69
1.42-1.460.21051530.19082758X-RAY DIFFRACTION98.74
1.46-1.510.19831400.15662766X-RAY DIFFRACTION98.94
1.51-1.550.1821380.13732767X-RAY DIFFRACTION99.15
1.55-1.610.15761570.13052744X-RAY DIFFRACTION99.08
1.61-1.670.19211220.13182778X-RAY DIFFRACTION99.11
1.67-1.750.17091580.12212758X-RAY DIFFRACTION99.28
1.75-1.840.18081380.12982799X-RAY DIFFRACTION99.66
1.84-1.960.15791440.13482800X-RAY DIFFRACTION99.8
1.96-2.110.1771350.14972785X-RAY DIFFRACTION99.9
2.11-2.320.19391420.13922808X-RAY DIFFRACTION99.93
2.32-2.660.18991450.14752808X-RAY DIFFRACTION99.9
2.66-3.350.18491490.15612814X-RAY DIFFRACTION99.7
3.35-24.10.18391410.14272852X-RAY DIFFRACTION99.37

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