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

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Basic information

Entry
Database: PDB / ID: 8smh
TitleChimeric ETS-domain of murine PU.1 harboring the corresponding beta-strand 3 (S3) residues from murine Ets-1 in complex with 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
KeywordsTRANSCRIPTION / transcription factor / protein-DNA complex / ETS family / ETS / PU.1 / TRANSCRIPTION-DNA complex
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 / lymphocyte 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 / lymphoid progenitor cell differentiation / immature B cell differentiation / myeloid dendritic cell differentiation / defense response to tumor cell / vasculature development / 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 / positive regulation of B cell differentiation / 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 / 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 / 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 / regulation of transcription by RNA polymerase II / chromatin / 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-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 speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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
DepositionApr 26, 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

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)22,3114
Polymers22,2883
Non-polymers231
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-27 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.944, 60.710, 45.066
Angle α, β, γ (deg.)90.000, 117.279, 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 / SFFV proviral integration 1 protein


Mass: 12491.681 Da / Num. of mol.: 1 / Fragment: ETS domain containing residues 167-272
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.: 267 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
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: 1.37→33.43 Å / Num. obs: 42457 / % possible obs: 98.01 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.56 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0383 / Rpim(I) all: 0.02466 / Rrim(I) all: 0.04571 / Net I/σ(I): 16.94
Reflection shellResolution: 1.37→1.419 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4507 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 4177 / CC1/2: 0.892 / CC star: 0.971 / Rpim(I) all: 0.2948 / Rrim(I) all: 0.5403 / % possible all: 96.77

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→33.43 Å / SU ML: 0.1736 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.6255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1772 1946 4.59 %
Rwork0.1432 40456 -
obs0.1447 42402 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.9 Å2
Refinement stepCycle: LAST / Resolution: 1.37→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms757 634 1 267 1659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821501
X-RAY DIFFRACTIONf_angle_d1.08142148
X-RAY DIFFRACTIONf_chiral_restr0.0621230
X-RAY DIFFRACTIONf_plane_restr0.0143160
X-RAY DIFFRACTIONf_dihedral_angle_d24.2058611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.38021330.35312839X-RAY DIFFRACTION96.56
1.4-1.440.26711560.23132843X-RAY DIFFRACTION97.12
1.44-1.480.19561270.15552876X-RAY DIFFRACTION97.06
1.48-1.530.18291510.13872838X-RAY DIFFRACTION97.71
1.53-1.590.16931240.15062864X-RAY DIFFRACTION97.65
1.59-1.650.21251370.14712891X-RAY DIFFRACTION97.9
1.65-1.730.1651370.12332868X-RAY DIFFRACTION97.69
1.73-1.820.16571380.12882876X-RAY DIFFRACTION98.21
1.82-1.930.18431410.1362906X-RAY DIFFRACTION98.67
1.93-2.080.18581430.14022905X-RAY DIFFRACTION98.8
2.08-2.290.15161470.13462923X-RAY DIFFRACTION98.87
2.29-2.620.18411410.13952920X-RAY DIFFRACTION99.13
2.62-3.30.18651350.15072938X-RAY DIFFRACTION98.62
3.3-33.430.1611360.13732969X-RAY DIFFRACTION98.29

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