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- PDB-5w3g: Solution Structure of ETS Transcription Factor PU.1 -

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Basic information

Entry
Database: PDB / ID: 5w3g
TitleSolution Structure of ETS Transcription Factor PU.1
ComponentsTranscription factor PU.1
KeywordsDNA BINDING PROTEIN / winged helix-turn-helix
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 / histone deacetylase binding / positive regulation of miRNA transcription / 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 / chromatin / regulation of DNA-templated transcription / positive regulation of gene expression / 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor PU.1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsLau, D.K.W. / Okon, M. / McIntosh, L.P.
CitationJournal: To be published
Title: Conserved protein dynamics within the ETS transcription factor family
Authors: Lau, D.K.W.
History
DepositionJun 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor PU.1


Theoretical massNumber of molelcules
Total (without water)12,9321
Polymers12,9321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8940 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription factor PU.1 / 31 kDa-transforming protein / SFFV proviral integration 1 protein


Mass: 12932.241 Da / Num. of mol.: 1 / Fragment: 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
161isotropic12D 1H-15N HSQC
171isotropic12D 1H-13C HSQC
181isotropic12D 1H-13C HSQC aliphatic
191isotropic12D 1H-13C HSQC aromatic
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY
1121isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.3 mM [U-99% 13C; U-99% 15N] DNA binding protein, 95% H2O/5% D2O
Label: 15N 13C / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.3 mM / Component: DNA binding protein / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 150mM KCL mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
NMReRyu H, Lim G, Sung BH, Lee J.refinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CYANAGuntert P.structure calculation
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: NMRe
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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