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- PDB-8sp1: Chimeric ETS-domain of murine PU.1 harboring the corresponding be... -

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Basic information

Entry
Database: PDB / ID: 8sp1
TitleChimeric ETS-domain of murine PU.1 harboring the corresponding beta-strand 3 (S3) residues from murine Ets-1 in complex with d(AATAAGCGIAAGTGGG)
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*GP*CP*GP*IP*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
KeywordsTRANSCRIPTION/DNA / transcription factor / protein-DNA complex / ETS family / ETS / PU.1 / TRANSCRIPTION-DNA complex / TRANSCRIPTION
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity ...positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / granulocyte differentiation / lymphocyte differentiation / apoptotic process involved in blood vessel morphogenesis / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation / immature B cell differentiation / negative regulation of MHC class II biosynthetic process / lymphoid progenitor cell differentiation / myeloid dendritic cell differentiation / vasculature development / regulation of DNA-binding transcription factor activity / oncogene-induced cell senescence / negative regulation of protein localization to chromatin / positive regulation of p38MAPK cascade / positive regulation of B cell differentiation / NFAT protein binding / somatic stem cell population maintenance / macrophage differentiation / cis-regulatory region sequence-specific DNA binding / lipopolysaccharide-mediated signaling pathway / transcription initiation-coupled chromatin remodeling / protein sequestering activity / erythrocyte differentiation / transforming growth factor beta receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / histone deacetylase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA 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 / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / 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 speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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: Structure / Year: 2024
Title: Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors.
Authors: Vernon, T.N. / Terrell, J.R. / Albrecht, A.V. / Germann, M.W. / Wilson, W.D. / Poon, G.M.K.
History
DepositionMay 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (5'-D(*AP*AP*TP*AP*AP*GP*CP*GP*IP*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)21,4374
Polymers21,4143
Non-polymers231
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-27 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.824, 60.725, 44.973
Angle α, β, γ (deg.)90.000, 117.272, 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*IP*AP*AP*GP*TP*GP*GP*G)-3')


Mass: 5021.277 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 / SFFV proviral integration 1 protein


Mass: 11632.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Spi1, Sfpi-1, Sfpi1 / Production host: Escherichia coli (E. coli) / References: UniProt: P17433
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Sodium Acetate, pH=4.6, 2% 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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2021
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→33.39 Å / Num. obs: 25881 / % possible obs: 98.86 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.73 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.04781 / Rpim(I) all: 0.0307 / Rrim(I) all: 0.057 / Net I/σ(I): 14.63
Reflection shellResolution: 1.62→1.678 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4136 / Mean I/σ(I) obs: 2.92 / Num. unique obs: 2541 / CC1/2: 0.958 / CC star: 0.989 / Rpim(I) all: 0.2641 / Rrim(I) all: 0.4921 / % possible all: 97.25

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→33.39 Å / SU ML: 0.1966 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.0529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1993 2018 7.82 %
Rwork0.1659 23799 -
obs0.1686 25817 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.92 Å2
Refinement stepCycle: LAST / Resolution: 1.62→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms757 633 1 258 1649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01141498
X-RAY DIFFRACTIONf_angle_d1.37962138
X-RAY DIFFRACTIONf_chiral_restr0.0651230
X-RAY DIFFRACTIONf_plane_restr0.0122160
X-RAY DIFFRACTIONf_dihedral_angle_d24.2042617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.35861280.30231685X-RAY DIFFRACTION97.42
1.66-1.710.32181560.27091641X-RAY DIFFRACTION97.24
1.71-1.760.26981220.22651678X-RAY DIFFRACTION97.88
1.76-1.810.24651580.19941686X-RAY DIFFRACTION98.77
1.81-1.880.21651350.17881701X-RAY DIFFRACTION98.87
1.88-1.950.22421410.18151716X-RAY DIFFRACTION98.78
1.95-2.040.21441560.18621674X-RAY DIFFRACTION99.46
2.04-2.150.22221340.16911714X-RAY DIFFRACTION99.41
2.15-2.280.20771400.16061718X-RAY DIFFRACTION99.52
2.28-2.460.1831410.15641692X-RAY DIFFRACTION99.57
2.46-2.710.17521570.16421728X-RAY DIFFRACTION99.89
2.71-3.10.20981560.17261702X-RAY DIFFRACTION99.57
3.1-3.90.19531510.1461702X-RAY DIFFRACTION98.46
3.9-33.390.15891430.14441762X-RAY DIFFRACTION99.43

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