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- PDB-8ek8: Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAGAAGGG) -

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Basic information

Entry
Database: PDB / ID: 8ek8
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAGAAGGG)
Components
  • DNA (5'-D(*AP*TP*AP*AP*AP*AP*GP*GP*AP*GP*AP*AP*GP*GP*G)-3')
  • DNA (5'-D(P*CP*CP*CP*TP*TP*CP*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 / pro-T cell differentiation / negative regulation of neutrophil degranulation / positive regulation of microglial cell mediated cytotoxicity / myeloid leukocyte differentiation / 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 / positive regulation of microglial cell mediated cytotoxicity / myeloid leukocyte differentiation / 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 / negative regulation of non-canonical NF-kappaB signal transduction / oncogene-induced cell senescence / negative regulation of protein localization to chromatin / positive regulation of p38MAPK cascade / positive regulation of B cell differentiation / DNA-binding transcription repressor activity / STAT family protein binding / DNA-binding transcription activator activity / negative regulation of NF-kappaB transcription factor activity / interleukin-6-mediated signaling pathway / NFAT protein binding / cis-regulatory region sequence-specific DNA binding / transcription initiation-coupled chromatin remodeling / protein sequestering activity / regulation of erythrocyte differentiation / positive regulation of miRNA transcription / Transcriptional regulation of granulopoiesis / histone deacetylase binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / molecular adaptor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / chromatin / regulation of DNA-templated transcription / 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 family / Ets-domain signature 2. / Ets domain / 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: 2.63 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 20, 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*TP*AP*AP*AP*AP*GP*GP*AP*GP*AP*AP*GP*GP*G)-3')
D: DNA (5'-D(P*CP*CP*CP*TP*TP*CP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
F: Transcription factor PU.1
A: DNA (5'-D(*AP*TP*AP*AP*AP*AP*GP*GP*AP*GP*AP*AP*GP*GP*G)-3')
B: DNA (5'-D(P*CP*CP*CP*TP*TP*CP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
E: Transcription factor PU.1


Theoretical massNumber of molelcules
Total (without water)43,8546
Polymers43,8546
Non-polymers00
Water0
1
C: DNA (5'-D(*AP*TP*AP*AP*AP*AP*GP*GP*AP*GP*AP*AP*GP*GP*G)-3')
D: DNA (5'-D(P*CP*CP*CP*TP*TP*CP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
F: Transcription factor PU.1


Theoretical massNumber of molelcules
Total (without water)21,9273
Polymers21,9273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA (5'-D(*AP*TP*AP*AP*AP*AP*GP*GP*AP*GP*AP*AP*GP*GP*G)-3')
B: DNA (5'-D(P*CP*CP*CP*TP*TP*CP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
E: Transcription factor PU.1


Theoretical massNumber of molelcules
Total (without water)21,9273
Polymers21,9273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.058, 61.064, 154.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 5053.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*CP*TP*TP*CP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')


Mass: 4436.882 Da / Num. of mol.: 2 / 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.: 2 / 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

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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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM Ammonium Acetate, 100 mM TRIS, pH=8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2021
RadiationMonochromator: Liquid nitrogen cooled dual crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.63→34.81 Å / Num. obs: 12962 / % possible obs: 98.71 % / Redundancy: 7 % / Biso Wilson estimate: 63.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0747 / Rpim(I) all: 0.08107 / Rrim(I) all: 0.03082 / Net I/σ(I): 17.17
Reflection shellResolution: 2.63→2.724 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.9361 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 1263 / CC1/2: 0.926 / CC star: 0.981 / Rpim(I) all: 1 / Rrim(I) all: 0.3744 / % possible all: 99.21

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8E3K

8e3k


Resolution: 2.63→34.81 Å / SU ML: 0.3822 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.8595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2797 1283 10.01 %
Rwork0.2367 11540 -
obs0.241 12823 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.42 Å2
Refinement stepCycle: LAST / Resolution: 2.63→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 1225 0 0 2709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332903
X-RAY DIFFRACTIONf_angle_d0.57964149
X-RAY DIFFRACTIONf_chiral_restr0.0349444
X-RAY DIFFRACTIONf_plane_restr0.0022310
X-RAY DIFFRACTIONf_dihedral_angle_d25.76351179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.740.41271380.36361258X-RAY DIFFRACTION99.22
2.74-2.860.39191400.3421249X-RAY DIFFRACTION98.86
2.86-3.010.37081410.3241262X-RAY DIFFRACTION98.73
3.01-3.20.35981360.29831219X-RAY DIFFRACTION96.51
3.2-3.450.32591420.26451273X-RAY DIFFRACTION98.47
3.45-3.790.28211430.26911265X-RAY DIFFRACTION98.39
3.79-4.340.27641410.23891295X-RAY DIFFRACTION99.1
4.34-5.460.23741460.21131317X-RAY DIFFRACTION99.73
5.46-34.810.22751560.17141402X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: -21.6320871553 Å / Origin y: -0.408787658335 Å / Origin z: 53.7470606754 Å
111213212223313233
T0.460674148045 Å2-0.0566927966378 Å20.00162214181923 Å2-0.567930226198 Å2-0.00317067284709 Å2--0.533475697261 Å2
L-0.179716817114 °2-0.28652130626 °2-0.148257428503 °2-0.605091058086 °20.569491430693 °2--4.2533926481 °2
S0.0756700208794 Å °-0.233585600611 Å °-0.0383864125483 Å °0.00896230851262 Å °0.00802547671761 Å °0.0100203785205 Å °-0.0421987923161 Å °0.217927641195 Å °-1.14772493228E-5 Å °
Refinement TLS groupSelection details: all

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