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

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Basic information

Entry
Database: PDB / ID: 8vdi
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAGAGGAAGTGGG) in Ternary Complex with DB2447
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*GP*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*CP*TP*TP*AP*T)-3')
  • Transcription factor PU.1
KeywordsTRANSCRIPTION/DNA / Minor groove binder / DNA binding small molecule / diamidine / PU.1 / transcription factor / transcriptional inhibition / TRANSCRIPTION / TRANSCRIPTION-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)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsTerrell, J.R. / Ogbonna, E.N. / Poon, G.M.K. / Wilson, W.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
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
CitationJournal: Rsc Adv / Year: 2024
Title: Single GC base pair recognition by a heterocyclic diamidine: structures, affinities, and dynamics.
Authors: Ogbonna, E.N. / Terrell, J.R. / Paul, A. / Farahat, A.A. / Poon, G.M.K. / Boykin, D.W. / Wilson, W.D.
History
DepositionDec 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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*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*CP*TP*TP*AP*T)-3')
F: Transcription factor PU.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6074
Polymers22,2323
Non-polymers3751
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-17 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.996, 60.583, 44.297
Angle α, β, γ (deg.)90.000, 116.635, 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*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')


Mass: 5060.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#2: DNA chain DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*CP*TP*TP*AP*T)-3')


Mass: 4735.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: Protein Transcription factor PU.1 / 31 kDa-transforming protein


Mass: 12436.583 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 (E. coli) / References: UniProt: P17947
#4: Chemical ChemComp-A1AAQ / 4,4'-[pyridine-2,6-diylbis(methyleneoxy)]di(benzene-1-carboximidamide)


Mass: 375.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100mM Sodium Acetate, pH=4.6, 2% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Jul 21, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→33.14 Å / Num. obs: 15325 / % possible obs: 99.44 % / Redundancy: 4.1 % / Biso Wilson estimate: 23.75 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.08503 / Rpim(I) all: 0.04789 / Rrim(I) all: 0.09787 / Net I/σ(I): 12.82
Reflection shellResolution: 1.93→1.999 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6843 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 1543 / CC1/2: 0.791 / CC star: 0.94 / Rpim(I) all: 0.3856 / Rrim(I) all: 0.7875 / % possible all: 99.87

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→33.14 Å / SU ML: 0.2048 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2018 769 5.03 %
Rwork0.1664 14531 -
obs0.1683 15300 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.84 Å2
Refinement stepCycle: LAST / Resolution: 1.93→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 634 28 182 1595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011515
X-RAY DIFFRACTIONf_angle_d1.24222164
X-RAY DIFFRACTIONf_chiral_restr0.059227
X-RAY DIFFRACTIONf_plane_restr0.015162
X-RAY DIFFRACTIONf_dihedral_angle_d24.01631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.080.2681850.21142876X-RAY DIFFRACTION99.84
2.08-2.290.24661150.19632920X-RAY DIFFRACTION99.8
2.29-2.620.2438940.17672968X-RAY DIFFRACTION99.74
2.62-3.30.19712040.17552851X-RAY DIFFRACTION99.16
3.3-33.140.17371710.13992916X-RAY DIFFRACTION98.85

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