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- PDB-3ri4: Ets1 cooperative binding to widely separated sites on promoter DNA -

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Basic information

Entry
Database: PDB / ID: 3ri4
TitleEts1 cooperative binding to widely separated sites on promoter DNA
Components
  • (TCR alpha promoter DNA) x 2
  • Isoform Ets-1 p27 of Protein C-ets-1
KeywordsTranscription/DNA / transcription / T-cell receptor alpha / DNA binding / autoinhibition / Ets domain / transcription factor / DNA / Runx2 / Runx1 / Transcription-DNA complex
Function / homology
Function and homology information


PML body organization / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / positive regulation of endothelial cell migration / transcription corepressor binding / nuclear receptor coactivator activity / positive regulation of erythrocyte differentiation / cell motility ...PML body organization / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / positive regulation of endothelial cell migration / transcription corepressor binding / nuclear receptor coactivator activity / positive regulation of erythrocyte differentiation / cell motility / Oncogene Induced Senescence / positive regulation of inflammatory response / positive regulation of miRNA transcription / positive regulation of angiogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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. / ETS family ...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. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C-ets-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBabayeva, N.D. / Mino, K. / Tahirov, T.H.
CitationJournal: Plos One / Year: 2012
Title: Structural basis of ets1 cooperative binding to widely separated sites on promoter DNA.
Authors: Babayeva, N.D. / Baranovskaya, O.I. / Tahirov, T.H.
History
DepositionApr 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Structure summary
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform Ets-1 p27 of Protein C-ets-1
B: TCR alpha promoter DNA
C: TCR alpha promoter DNA
D: Isoform Ets-1 p27 of Protein C-ets-1
E: TCR alpha promoter DNA
F: TCR alpha promoter DNA


Theoretical massNumber of molelcules
Total (without water)57,4726
Polymers57,4726
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-63 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.177, 98.124, 53.577
Angle α, β, γ (deg.)90.00, 109.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoform Ets-1 p27 of Protein C-ets-1


Mass: 18938.465 Da / Num. of mol.: 2 / Fragment: UNP residues 280-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETS1 / Plasmid: PETS280-441 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14921
#2: DNA chain TCR alpha promoter DNA


Mass: 4843.156 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain TCR alpha promoter DNA


Mass: 4954.214 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 295 K / Method: sitting drop vapor diffusion, macroseeding / pH: 8.5
Details: 200 mM ammonium chloride, 10 mM calcium chloride, 50 mM Tris-HCl buffer (pH 8.5), 18.5% v/v PEG MME 2000, 3% v/v glycerol, sitting drop vapor diffusion and macroseeding, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 9369 / % possible obs: 94.7 % / Observed criterion σ(I): -1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.2 / Num. unique all: 858 / % possible all: 87.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1gvj

1gvj


Resolution: 3→29.84 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1515668.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 446 5.3 %RANDOM
Rwork0.23 ---
obs0.23 8427 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.1762 Å2 / ksol: 0.282842 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.97 Å20 Å23.88 Å2
2--7.59 Å20 Å2
3----2.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 1300 0 33 3567
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.721.5
X-RAY DIFFRACTIONc_mcangle_it5.92
X-RAY DIFFRACTIONc_scbond_it5.222
X-RAY DIFFRACTIONc_scangle_it7.662.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 70 5.3 %
Rwork0.342 1243 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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