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- PDB-8e5y: Human PU.1 ETS-Domain Bound to d(AATAAGCGGAAGTGGG) Acetate Free a... -

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Basic information

Entry
Database: PDB / ID: 8e5y
TitleHuman PU.1 ETS-Domain Bound to d(AATAAGCGGAAGTGGG) Acetate Free at pH 5.4
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 / 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: 1.32 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 22, 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)22,2564
Polymers22,2333
Non-polymers231
Water4,594255
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)43.059, 60.807, 44.437
Angle α, β, γ (deg.)90.000, 116.242, 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: 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*AP*CP*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: Expression vector pET-mod (others) / 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.: 255 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 100 mM Bis-Tris pH 5.4, 2% PEG 3350

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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 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→32.6 Å / Num. obs: 47335 / % possible obs: 97.93 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.49 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.04438 / Rpim(I) all: 0.0272 / Rrim(I) all: 0.05238 / Net I/σ(I): 15.84
Reflection shellResolution: 1.32→1.367 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3501 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4710 / CC1/2: 0.928 / CC star: 0.981 / Rpim(I) all: 0.2048 / Rrim(I) all: 0.4076 / % possible all: 98.37

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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: 1.32→32.6 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.5733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1624 1979 4.19 %
Rwork0.1485 45304 -
obs0.1491 47283 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.08 Å2
Refinement stepCycle: LAST / Resolution: 1.32→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 634 1 255 1641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911492
X-RAY DIFFRACTIONf_angle_d1.17912135
X-RAY DIFFRACTIONf_chiral_restr0.07228
X-RAY DIFFRACTIONf_plane_restr0.0136159
X-RAY DIFFRACTIONf_dihedral_angle_d23.7968610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.350.20911280.20323258X-RAY DIFFRACTION98.32
1.35-1.390.1871440.17023234X-RAY DIFFRACTION98.34
1.39-1.430.18851560.15873206X-RAY DIFFRACTION98.19
1.43-1.480.13141260.14553222X-RAY DIFFRACTION97.69
1.48-1.530.14131450.12363233X-RAY DIFFRACTION98.28
1.53-1.590.13261370.12133282X-RAY DIFFRACTION99.13
1.59-1.660.12991490.12173246X-RAY DIFFRACTION98.81
1.66-1.750.11711490.12473184X-RAY DIFFRACTION97.97
1.75-1.860.14721310.1283278X-RAY DIFFRACTION97.93
1.86-20.14771470.14433180X-RAY DIFFRACTION96.83
2-2.210.16741420.14953253X-RAY DIFFRACTION98.58
2.21-2.520.15141560.14783266X-RAY DIFFRACTION98.9
2.53-3.180.1821400.16563262X-RAY DIFFRACTION97.9
3.18-32.60.17181290.15013200X-RAY DIFFRACTION94.39

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