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- PDB-9cmb: Human PU.1 ETS Domain (165-270) bound to d(AATAAAAGGAAGTGGG) -

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Basic information

Entry
Database: PDB / ID: 9cmb
TitleHuman PU.1 ETS Domain (165-270) bound to d(AATAAAAGGAAGTGGG)
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
KeywordsDNA BINDING PROTEIN/DNA / ETS family transcription factor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 / 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: 2.15 Å
AuthorsPoon, G.M.K.
Funding support United States, 3items
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137160 United States
CitationJournal: To Be Published
Title: Human PU.1 ETS Domain (165-270) bound to d(AATAAAAGGAAGTGGG)
Authors: Poon, G.M.K.
History
DepositionJul 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,5277
Polymers44,4626
Non-polymers651
Water1,69394
1
A: Transcription factor PU.1
B: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
E: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,2313
Polymers22,2313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-23 kcal/mol
Surface area9820 Å2
MethodPISA
2
C: Transcription factor PU.1
D: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
F: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2964
Polymers22,2313
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-50 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.954, 102.731, 55.753
Angle α, β, γ (deg.)90.000, 111.651, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21C-426-

HOH

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Components

#1: 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 BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P17947
#2: 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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, pH 6.5, 200 mM zinc acetate and 2% PEG 600

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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, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920119 Å / Relative weight: 1
ReflectionResolution: 2.15→28.91 Å / Num. obs: 25670 / % possible obs: 99.09 % / Redundancy: 1.8 % / Biso Wilson estimate: 42.47 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.053 / Rrim(I) all: 0.075 / Net I/σ(I): 7.6
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2547 / CC1/2: 0.78 / CC star: 0.943 / Rpim(I) all: 0.478 / Rrim(I) all: 0.676 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→28.91 Å / SU ML: 0.3025 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 3658 7.75 %
Rwork0.2332 43571 -
obs0.2342 25670 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.93 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 1300 1 94 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01463002
X-RAY DIFFRACTIONf_angle_d1.55284298
X-RAY DIFFRACTIONf_chiral_restr0.1460
X-RAY DIFFRACTIONf_plane_restr0.0096316
X-RAY DIFFRACTIONf_dihedral_angle_d25.9741298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.36041340.36851586X-RAY DIFFRACTION88.84
2.18-2.210.35411390.35871653X-RAY DIFFRACTION90.51
2.21-2.240.28551330.34021614X-RAY DIFFRACTION88.68
2.24-2.270.32461410.31311622X-RAY DIFFRACTION90.23
2.27-2.310.36121400.28591647X-RAY DIFFRACTION90.94
2.31-2.350.28881420.31031648X-RAY DIFFRACTION91
2.35-2.390.31591350.28991641X-RAY DIFFRACTION90.98
2.39-2.430.30891430.28281652X-RAY DIFFRACTION91.4
2.43-2.480.29581300.29271659X-RAY DIFFRACTION91.46
2.48-2.530.27851420.27571657X-RAY DIFFRACTION91.79
2.53-2.580.29061420.24841690X-RAY DIFFRACTION92.29
2.58-2.640.2851380.27151699X-RAY DIFFRACTION92.59
2.64-2.710.30591340.26841644X-RAY DIFFRACTION92.41
2.71-2.780.30251360.28671666X-RAY DIFFRACTION92.51
2.78-2.860.29971430.2671712X-RAY DIFFRACTION92.66
2.86-2.960.25911410.26721647X-RAY DIFFRACTION92.45
2.96-3.060.30631430.28531695X-RAY DIFFRACTION93.73
3.06-3.180.35411430.27021670X-RAY DIFFRACTION93.36
3.18-3.330.21151430.23151706X-RAY DIFFRACTION92.73
3.33-3.50.21681450.2131696X-RAY DIFFRACTION93.22
3.5-3.720.24771420.20741691X-RAY DIFFRACTION94.58
3.72-4.010.22211400.19211719X-RAY DIFFRACTION93.7
4.01-4.410.17321410.15821679X-RAY DIFFRACTION95.04
4.41-5.050.19511510.19081752X-RAY DIFFRACTION96.11
5.05-6.350.22821450.22031766X-RAY DIFFRACTION97.2
6.35-28.910.21361520.22351760X-RAY DIFFRACTION96.86

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