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

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Basic information

Entry
Database: PDB / ID: 8ufk
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGCGGAAGTG)
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')
  • Transcription factor PU.1
KeywordsTRANSCRIPTION / transcription factor / protein-DNA complex / ETS family / ETS / PU.1 / TRANSCRIPTION-DNA complex / diamidine / minor-groove binder / small-molecule / transcription inhibition
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: 2.41 Å
AuthorsTerrell, J.R. / Poon, G.M.K. / Wilson, W.D.
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: To Be Published
Title: Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders
Authors: Terrell, J.R. / Paul, A. / Ogbonna, E.N. / Farahat, A.A. / Poon, G.M.K. / Wilson, W.D.
History
DepositionOct 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,4626
Polymers44,4626
Non-polymers00
Water905
1
A: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*G)-3')
B: DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*G)-3')
D: DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')
E: Transcription factor PU.1


Theoretical massNumber of molelcules
Total (without water)22,2313
Polymers22,2313
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.459, 70.714, 58.879
Angle α, β, γ (deg.)90.000, 113.997, 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*CP*GP*GP*AP*AP*GP*TP*G)-3')


Mass: 5004.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')


Mass: 4790.113 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 48.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM TRIS Base (HCl adjusted), pH=8.5, 200mM Ammonium Acetate, 24% PEG3350 1:1 hanging drop with 250uM protein/DNA complex

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.920119 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationMonochromator: Horizontal double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920119 Å / Relative weight: 1
ReflectionResolution: 2.41→31.1 Å / Num. obs: 16100 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 61.47 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Net I/σ(I): 9.5
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2 / Num. unique obs: 1678 / CC1/2: 0.947 / Rpim(I) all: 0.295 / Rrim(I) all: 0.693 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→31.1 Å / SU ML: 0.3696 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.2841
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 1571 9.95 %
Rwork0.2276 14211 -
obs0.2315 15782 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.61 Å2
Refinement stepCycle: LAST / Resolution: 2.41→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 1300 0 5 2782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362963
X-RAY DIFFRACTIONf_angle_d0.64174249
X-RAY DIFFRACTIONf_chiral_restr0.039457
X-RAY DIFFRACTIONf_plane_restr0.0027311
X-RAY DIFFRACTIONf_dihedral_angle_d25.67261191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.490.42491360.35181271X-RAY DIFFRACTION96.37
2.49-2.580.38081430.31671269X-RAY DIFFRACTION97.11
2.58-2.680.32361290.31491290X-RAY DIFFRACTION98.34
2.68-2.80.44481510.35591306X-RAY DIFFRACTION98.11
2.8-2.950.37921420.33331283X-RAY DIFFRACTION97.54
2.95-3.130.35991390.30791261X-RAY DIFFRACTION96.49
3.13-3.380.32071470.28521222X-RAY DIFFRACTION93.13
3.38-3.710.30721310.24741312X-RAY DIFFRACTION97.11
3.71-4.250.24141570.2151305X-RAY DIFFRACTION99.59
4.25-5.350.22461450.19091332X-RAY DIFFRACTION99.73
5.35-31.10.19451510.15771360X-RAY DIFFRACTION99.87

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