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- PDB-2nny: Crystal structure of the Ets1 dimer DNA complex. -

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Basic information

Entry
Database: PDB / ID: 2nny
TitleCrystal structure of the Ets1 dimer DNA complex.
Components
  • 5'-D(*A*CP*TP*CP*CP*AP*GP*GP*AP*AP*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*TP*CP*T)-3'
  • 5'-D(*T*AP*GP*AP*CP*AP*GP*GP*AP*AP*GP*CP*AP*CP*TP*TP*CP*CP*TP*GP*GP*AP*G)-3'
  • C-ets-1 protein
KeywordsTranscription/DNA / ETS-1 / PROTEIN-DNA COMPLEX / 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 / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / 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 / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / cell motility / Oncogene Induced Senescence / positive regulation of miRNA transcription / positive regulation of inflammatory response / 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 / positive regulation of gene expression / chromatin / 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: 2.58 Å
AuthorsLamber, E.P. / Kachalova, G.S. / Wilmanns, M.
CitationJournal: Embo J. / Year: 2008
Title: Regulation of the transcription factor Ets-1 by DNA-mediated homo-dimerization.
Authors: Lamber, E.P. / Vanhille, L. / Textor, L.C. / Kachalova, G.S. / Sieweke, M.H. / Wilmanns, M.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 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

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*T*AP*GP*AP*CP*AP*GP*GP*AP*AP*GP*CP*AP*CP*TP*TP*CP*CP*TP*GP*GP*AP*G)-3'
D: 5'-D(*A*CP*TP*CP*CP*AP*GP*GP*AP*AP*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*TP*CP*T)-3'
A: C-ets-1 protein
B: C-ets-1 protein


Theoretical massNumber of molelcules
Total (without water)53,8794
Polymers53,8794
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.556, 100.838, 69.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 7114.611 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*A*CP*TP*CP*CP*AP*GP*GP*AP*AP*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*TP*CP*T)-3'


Mass: 7007.520 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein C-ets-1 protein / p54


Mass: 19878.463 Da / Num. of mol.: 2 / Fragment: residues 280-441 / Mutation: C350S , C416S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETS1 / Plasmid: PETM10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P14921
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium acetate 28% PEG 2000 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium acetate11
2PEG 200011
3sodium citrate11
4H2O11
5ammonium acetate12
6PEG 200012
7sodium citrate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2005
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.58→19.96 Å / Num. all: 21423 / Num. obs: 20507 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.45

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K79

1k79


Resolution: 2.58→19.69 Å / Isotropic thermal model: Isotropic / Cross valid method: R-FREE / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2712 1041 RANDOM
Rwork0.2353 --
all-20497 -
obs-19446 -
Displacement parametersBiso mean: 32.3 Å2
Refinement stepCycle: LAST / Resolution: 2.58→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 896 0 46 3060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00613
X-RAY DIFFRACTIONc_angle_deg1.20032

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