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- PDB-3wu1: Crystal structure of the ETS1-RUNX1-DNA ternary complex -

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Basic information

Entry
Database: PDB / ID: 3wu1
TitleCrystal structure of the ETS1-RUNX1-DNA ternary complex
Components
  • DNA (5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')
  • DNA (5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')
  • Protein C-ets-1
  • Runt-related transcription factor 1
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DNA-BINDING / METHYLATION / NUCLEUS / PHOSPHOPROTEIN / TRANSCRIPTION REGULATION / ISOPEPTIDE BOND / PROTO-ONCOGENE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of hair follicle cell proliferation / SLC-mediated transport of organic cations / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / core-binding factor complex ...regulation of hair follicle cell proliferation / SLC-mediated transport of organic cations / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / core-binding factor complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of CD8-positive, alpha-beta T cell differentiation / positive regulation of cell maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / PML body organization / neuron fate commitment / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / definitive hemopoiesis / regulation of T cell anergy / central nervous system neuron differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / embryonic hemopoiesis / hair follicle morphogenesis / negative regulation of cell cycle / behavioral response to pain / hemopoiesis / basement membrane / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / regulation of signal transduction / response to retinoic acid / neuron development / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / central nervous system development / transcription corepressor binding / skeletal system development / cell motility / liver development / Oncogene Induced Senescence / positive regulation of miRNA transcription / positive regulation of type II interferon production / neuron differentiation / positive regulation of angiogenesis / positive regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / gene expression / DNA-binding transcription factor binding / in utero embryonic development / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / response to antibiotic / negative regulation of DNA-templated transcription / 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 / protein-containing complex / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Protein C-ets-1, pointed domain / Transforming protein C-ets ...Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Immunoglobulin-like - #720 / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Sterile alpha motif/pointed domain superfamily / 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 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C-ets-1 / Runt-related transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTahirov, T.H. / Ogata, K.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions.
Authors: Shiina, M. / Hamada, K. / Inoue-Bungo, T. / Shimamura, M. / Uchiyama, A. / Baba, S. / Sato, K. / Yamamoto, M. / Ogata, K.
History
DepositionApr 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Runt-related transcription factor 1
B: Protein C-ets-1
C: DNA (5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')
D: DNA (5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)36,3094
Polymers36,3094
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-31 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.278, 140.902, 95.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Runt-related transcription factor 1 / Acute myeloid leukemia 1 protein / Core-binding factor subunit alpha-2 / CBF-alpha-2 / Oncogene AML- ...Acute myeloid leukemia 1 protein / Core-binding factor subunit alpha-2 / CBF-alpha-2 / Oncogene AML-1 / Polyomavirus enhancer-binding protein 2 alpha B subunit / PEA2-alpha B / PEBP2-alpha B / SL3-3 enhancer factor 1 alpha B subunit / SL3/AKV core-binding factor alpha B subunit


Mass: 13540.438 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 55-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aml1, Cbfa2, Pebp2ab, Runx1 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03347
#2: Protein Protein C-ets-1 / p54


Mass: 12970.817 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 333-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETS1, EWSR2 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14921
#3: DNA chain DNA (5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')


Mass: 4843.156 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')


Mass: 4954.214 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 4.75 Å3/Da / Density % sol: 74.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 11% PEG MME 550, 0.1M KCL, 0.015M MGCL2, 0.05M TRIS, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 23925 / % possible obs: 87.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.352 / % possible all: 65.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IO4, 1GVJ

1io4

1gvj


Resolution: 2.4→29.78 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.249 1158 4.2 %
Rwork0.213 --
obs0.213 23807 86.9 %
Solvent computationBsol: 38.09 Å2
Displacement parametersBiso mean: 46.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.391 Å20 Å20 Å2
2--1.53 Å20 Å2
3----0.139 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 650 0 138 2624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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