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- PDB-8uff: Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAAGTGGG) in T... -

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Basic information

Entry
Database: PDB / ID: 8uff
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAAGTGGG) in Ternary Complex with DB1976
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*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: 1.66 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,6784
Polymers22,2313
Non-polymers4471
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-18 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.913, 60.292, 44.393
Angle α, β, γ (deg.)90.000, 116.358, 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*GP*AP*AP*GP*TP*GP*GP*G)-3')


Mass: 5044.317 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*TP*TP*TP*TP*AP*T)-3')


Mass: 4750.089 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-Y5U / (2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide)


Mass: 447.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16N8Se / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM Sodium Acetate, pH=4.6, 2% PEG 3350 well solution mixed 1:1 with 250uM Protein/DNA Complex

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2021
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.66→33.2 Å / Num. obs: 23969 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.47 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04366 / Rpim(I) all: 0.02639 / Rrim(I) all: 0.05122 / Net I/σ(I): 17.45
Reflection shellResolution: 1.66→1.719 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3469 / Mean I/σ(I) obs: 3.71 / Num. unique obs: 2414 / CC1/2: 0.956 / CC star: 0.989 / Rpim(I) all: 0.1995 / Rrim(I) all: 0.4013 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→33.2 Å / SU ML: 0.1859 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201 1978 8.27 %
Rwork0.1624 21954 -
obs0.1658 23932 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.41 Å2
Refinement stepCycle: LAST / Resolution: 1.66→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 634 29 230 1644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01011509
X-RAY DIFFRACTIONf_angle_d1.33962160
X-RAY DIFFRACTIONf_chiral_restr0.0583226
X-RAY DIFFRACTIONf_plane_restr0.0124161
X-RAY DIFFRACTIONf_dihedral_angle_d24.3418625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.28231360.21861564X-RAY DIFFRACTION99.24
1.7-1.750.22571400.19891554X-RAY DIFFRACTION99.65
1.75-1.80.2491410.19951566X-RAY DIFFRACTION99.77
1.8-1.860.24211470.18481559X-RAY DIFFRACTION99.71
1.86-1.920.23811420.18471556X-RAY DIFFRACTION99.59
1.92-20.21561340.18121591X-RAY DIFFRACTION100
2-2.090.22451330.18231559X-RAY DIFFRACTION99.88
2.09-2.20.21781400.16771566X-RAY DIFFRACTION99.88
2.2-2.340.19491500.15481576X-RAY DIFFRACTION99.65
2.34-2.520.19191460.16131553X-RAY DIFFRACTION99.77
2.52-2.770.22081430.17051568X-RAY DIFFRACTION99.59
2.77-3.170.21281470.17231573X-RAY DIFFRACTION99.54
3.17-40.1781370.14311565X-RAY DIFFRACTION98.21
4-33.20.17161420.14221604X-RAY DIFFRACTION98.98

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