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- PDB-1k7a: Ets-1(331-440)+GGAG duplex -

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Basic information

Entry
Database: PDB / ID: 1k7a
TitleEts-1(331-440)+GGAG duplex
Components
  • C-ets-1 Protein
  • DNA (5'-D(*CP*AP*CP*AP*TP*CP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*GP*AP*TP*GP*T)-3')
KeywordsTRANSCRIPTION/DNA / ETS domain / transcription factor / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Oncogene Induced Senescence / PML body organization / regulation of extracellular matrix disassembly / positive regulation of leukocyte adhesion to vascular endothelial cell / histone acetyltransferase binding / immune system process / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / positive regulation of endothelial cell migration ...Oncogene Induced Senescence / PML body organization / regulation of extracellular matrix disassembly / positive regulation of leukocyte adhesion to vascular endothelial cell / histone acetyltransferase binding / immune system process / 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 / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of miRNA transcription / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / response to antibiotic / positive regulation of cell population proliferation / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGarvie, C.W. / Hagman, J. / Wolberger, C.
CitationJournal: Mol.Cell / Year: 2001
Title: Structural studies of Ets-1/Pax5 complex formation on DNA.
Authors: Garvie, C.W. / Hagman, J. / Wolberger, C.
History
DepositionOct 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*GP*AP*TP*GP*T)-3')
C: DNA (5'-D(*CP*AP*CP*AP*TP*CP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
E: DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*GP*AP*TP*GP*T)-3')
F: DNA (5'-D(*CP*AP*CP*AP*TP*CP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
A: C-ets-1 Protein
D: C-ets-1 Protein


Theoretical massNumber of molelcules
Total (without water)44,2826
Polymers44,2826
Non-polymers00
Water0
1
B: DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*GP*AP*TP*GP*T)-3')
C: DNA (5'-D(*CP*AP*CP*AP*TP*CP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
A: C-ets-1 Protein


Theoretical massNumber of molelcules
Total (without water)22,1413
Polymers22,1413
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*GP*AP*TP*GP*T)-3')
F: DNA (5'-D(*CP*AP*CP*AP*TP*CP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
D: C-ets-1 Protein


Theoretical massNumber of molelcules
Total (without water)22,1413
Polymers22,1413
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.040, 75.270, 79.430
Angle α, β, γ (deg.)90.00, 118.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*GP*AP*TP*GP*T)-3')


Mass: 4665.032 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*CP*AP*TP*CP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')


Mass: 4489.925 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein C-ets-1 Protein


Mass: 12985.833 Da / Num. of mol.: 2 / Fragment: ETS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ets-1 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27577

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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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4M-1.6M Sodium Citrate, 100mM Hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium citrate11
2Hepes11
Crystal grow
*PLUS
pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 mMDNA1drop
21.4-1.6 Msodium citrate1reservoir
3100 mMHEPES1reservoirpH6.5
4100 mMacetate buffer1reservoirpH4.6
520 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 16, 2001 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→17.04 Å / Num. all: 11730 / Num. obs: 11730 / % possible obs: 0.969 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 76.7 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.8→2.93 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.8 / % possible all: 0.989
Reflection
*PLUS
% possible obs: 96.9 %
Reflection shell
*PLUS
% possible obs: 98.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→17.04 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 785098.7 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1124 10.2 %RANDOM
Rwork0.224 ---
all0.232 10964 --
obs0.232 10964 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.2093 Å2 / ksol: 0.363148 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-3.12 Å2
2--3.81 Å20 Å2
3----4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→17.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 1195 0 0 2945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d1.17
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 181 -
Rwork0.355 0 -
obs--0.931 %
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
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 17.7 Å / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.274
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor Rfree: 0.396 / Rfactor Rwork: 0.355

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