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

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Basic information

Entry
Database: PDB / ID: 8vdh
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAGAAGGAAGTGGG) in Ternary Complex with DB2447
Components
  • DNA (5'-D(*AP*AP*TP*AP*GP*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*CP*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 / 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 / TRAIL-activated apoptotic signaling pathway / granulocyte differentiation / endothelial to hematopoietic transition / negative regulation of adipose tissue development / apoptotic process involved in blood vessel morphogenesis / pericyte cell differentiation / negative regulation of MHC class II biosynthetic process / immature B cell differentiation / myeloid dendritic cell differentiation / defense response to tumor cell / 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 / DNA-binding transcription repressor activity / STAT family protein binding / DNA-binding transcription activator activity / 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 / transcription initiation-coupled chromatin remodeling / transforming growth factor beta receptor signaling pathway / 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 / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 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 / 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 transcription by RNA polymerase II / regulation of DNA-templated transcription / 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: 1.64 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,6074
Polymers22,2323
Non-polymers3751
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-23 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.049, 61.062, 44.178
Angle α, β, γ (deg.)90.000, 116.306, 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*GP*AP*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*TP*CP*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 / 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 (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.: 216 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2022
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.64→24.18 Å / Num. obs: 25020 / % possible obs: 97.21 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.88 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.06574 / Rpim(I) all: 0.0366 / Rrim(I) all: 0.07556 / Net I/σ(I): 11.37
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.93 / Num. unique obs: 2501 / CC1/2: 0.97 / CC star: 0.992 / Rpim(I) all: 0.1676 / Rrim(I) all: 0.3482 / % possible all: 98.84

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→24.18 Å / SU ML: 0.1512 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 1932 7.89 %
Rwork0.1819 22558 -
obs0.184 24490 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.28 Å2
Refinement stepCycle: LAST / Resolution: 1.64→24.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms757 634 28 216 1635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921521
X-RAY DIFFRACTIONf_angle_d1.22632171
X-RAY DIFFRACTIONf_chiral_restr0.0569227
X-RAY DIFFRACTIONf_plane_restr0.0117163
X-RAY DIFFRACTIONf_dihedral_angle_d24.4647636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.27271350.22161612X-RAY DIFFRACTION98.7
1.68-1.730.25391560.2081626X-RAY DIFFRACTION99.28
1.73-1.780.2371190.20961665X-RAY DIFFRACTION99.44
1.78-1.830.25651440.20951628X-RAY DIFFRACTION99.77
1.83-1.90.26581360.23231629X-RAY DIFFRACTION98.38
1.9-1.980.41191150.31941331X-RAY DIFFRACTION80.6
1.98-2.070.23351500.20471640X-RAY DIFFRACTION99.89
2.07-2.170.26911230.21341664X-RAY DIFFRACTION99.78
2.18-2.310.27441330.23341477X-RAY DIFFRACTION89
2.31-2.490.23031360.18151652X-RAY DIFFRACTION100
2.49-2.740.19971510.18061656X-RAY DIFFRACTION99.89
2.74-3.130.21721400.18021651X-RAY DIFFRACTION99.5
3.14-3.950.17461410.15481643X-RAY DIFFRACTION97.7
3.95-24.180.14251530.14141684X-RAY DIFFRACTION99.51

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