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- PDB-3mfk: Ets1 complex with stromelysin-1 promoter DNA -

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Basic information

Entry
Database: PDB / ID: 3mfk
TitleEts1 complex with stromelysin-1 promoter DNA
Components
  • (stromelysin-1 promoter DNA) x 2
  • Protein C-ets-1
KeywordsTRANSCRIPTION/DNA / Ets1 / Ets domain / protein-DNA complex / stromelysin-1 / 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: Cell Cycle / Year: 2010
Title: Structural basis of Ets1 cooperative binding to palindromic sequences on stromelysin-1 promoter DNA.
Authors: Babayeva, N.D. / Wilder, P.J. / Shiina, M. / Mino, K. / Desler, M. / Ogata, K. / Rizzino, A. / Tahirov, T.H.
History
DepositionApr 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein C-ets-1
B: Protein C-ets-1
C: stromelysin-1 promoter DNA
D: stromelysin-1 promoter DNA


Theoretical massNumber of molelcules
Total (without water)47,2604
Polymers47,2604
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-30 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.812, 99.153, 76.496
Angle α, β, γ (deg.)90.00, 108.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein C-ets-1 / p54


Mass: 18731.172 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, EWSR2 / Plasmid: pEts280-441 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14921
#2: DNA chain stromelysin-1 promoter DNA


Mass: 4914.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: stromelysin-1 promoter DNA sequence
#3: DNA chain stromelysin-1 promoter DNA


Mass: 4883.180 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: stromelysin-1 promoter DNA containing palindromic Ets-binding sequences
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.54 Å3/Da / Density % sol: 65.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15 mM ammonium chloride, 15 mM magnesium chloride, 0.7 M NDSB-195, 40 mM MES buffer (pH 6.5) and 11.5% v/v 2-Propanol, VAPOR DIFFUSION, SITTING DROP, temperature 295 K

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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 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 13212 / % possible obs: 97.9 % / Observed criterion σ(I): -2 / Redundancy: 3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 29.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.46 / Num. unique all: 1292 / % possible all: 96.1

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Processing

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

1gvj


Resolution: 3→36.35 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 3197409.06 / 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
Rfree0.289 631 5 %RANDOM
Rwork0.243 ---
obs0.243 12574 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3101 Å2 / ksol: 0.294203 e/Å3
Displacement parametersBiso mean: 71.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å27.91 Å2
2--3.15 Å20 Å2
3----3.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 650 0 27 2924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it4.781.5
X-RAY DIFFRACTIONc_mcangle_it7.522
X-RAY DIFFRACTIONc_scbond_it6.752
X-RAY DIFFRACTIONc_scangle_it9.352.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.44 106 5.5 %
Rwork0.419 1827 -
obs--87.6 %
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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