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- PDB-9ck2: Human PU.1 minimal ETS Domain (165-258) bound to d(AATAAGCGGAAGTGGG) -

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Basic information

Entry
Database: PDB / ID: 9ck2
TitleHuman PU.1 minimal ETS Domain (165-258) bound to d(AATAAGCGGAAGTGGG)
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
KeywordsDNA BINDING PROTEIN / ETS family transcription factor
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 / oncogene-induced cell senescence / regulation of DNA-binding transcription factor activity / positive regulation of p38MAPK cascade / negative regulation of non-canonical NF-kappaB signal transduction / negative regulation of protein localization to chromatin / positive regulation of B cell differentiation / DNA-binding transcription repressor activity / STAT family protein binding / DNA-binding transcription activator activity / interleukin-6-mediated signaling pathway / NFAT protein binding / negative regulation of NF-kappaB transcription factor activity / cis-regulatory region sequence-specific DNA binding / transcription initiation-coupled chromatin remodeling / protein sequestering activity / 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 / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / 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: 1.71 Å
AuthorsPoon, G.M.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL155178 United States
National Science Foundation (NSF, United States)MCB 2028902 United States
CitationJournal: To Be Published
Title: Human PU.1 minimal ETS Domain (165-258) bound to d(AATAAGCGGAAGTGGG)
Authors: Poon, G.M.K.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: 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*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)20,8864
Polymers20,8633
Non-polymers231
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-33 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.871, 60.569, 44.292
Angle α, β, γ (deg.)90.000, 116.593, 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: 11067.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPI1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / 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.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2% PEG 3350, 100 mM Sodium Acetate, pH 4.6

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.71→33.15 Å / Num. obs: 21885 / % possible obs: 99.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.025 / Rrim(I) all: 0.036 / Net I/σ(I): 13.2
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2191 / CC1/2: 0.964 / Rpim(I) all: 0.158 / Rrim(I) all: 0.223 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→33.15 Å / SU ML: 0.1603 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.5874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1839 1965 8.99 %
Rwork0.1503 19891 -
obs0.1533 21856 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.13 Å2
Refinement stepCycle: LAST / Resolution: 1.71→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms746 634 1 287 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00981487
X-RAY DIFFRACTIONf_angle_d1.24392128
X-RAY DIFFRACTIONf_chiral_restr0.0602227
X-RAY DIFFRACTIONf_plane_restr0.0124158
X-RAY DIFFRACTIONf_dihedral_angle_d24.4372609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.23921430.19061390X-RAY DIFFRACTION99.48
1.75-1.80.19881430.18351415X-RAY DIFFRACTION99.74
1.8-1.850.21541450.16781436X-RAY DIFFRACTION99.81
1.85-1.910.18461410.16591401X-RAY DIFFRACTION99.94
1.91-1.980.1871330.16511419X-RAY DIFFRACTION99.55
1.98-2.060.22011440.15991423X-RAY DIFFRACTION100
2.06-2.150.2031360.16011431X-RAY DIFFRACTION99.75
2.15-2.270.19051370.16191428X-RAY DIFFRACTION99.68
2.27-2.410.17721460.15181415X-RAY DIFFRACTION99.68
2.41-2.60.18961400.15191416X-RAY DIFFRACTION99.74
2.6-2.860.19221370.15871447X-RAY DIFFRACTION99.69
2.86-3.270.1791430.14811403X-RAY DIFFRACTION98.6
3.27-4.120.16251400.13281410X-RAY DIFFRACTION98.1
4.12-33.150.16641370.13221457X-RAY DIFFRACTION98.33

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