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- PDB-3wtz: Crystal structure of ETS-1 DNA binding and autoinhibitory domains... -

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Basic information

Entry
Database: PDB / ID: 3wtz
TitleCrystal structure of ETS-1 DNA binding and autoinhibitory domains (276-441)
ComponentsProtein C-ets-1
KeywordsTRANSCRIPTION / ETS-1 / AUTOINHIBITION / ETS DOMAIN / DNA-BINDING / ISOPEPTIDE BOND / NUCLEUS / PHOSPHOPROTEIN / PROTO-ONCOGENE / TRANSCRIPTION REGULATION
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 / positive regulation of erythrocyte differentiation / transcription corepressor binding / 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 / positive regulation of erythrocyte differentiation / transcription corepressor binding / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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-domain signature 2. ...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-domain signature 2. / Ets domain / ETS family / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsShiina, M. / Hamada, K. / 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

Downloads & links

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Assembly

Deposited unit
A: Protein C-ets-1
B: Protein C-ets-1


Theoretical massNumber of molelcules
Total (without water)38,4332
Polymers38,4332
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-10 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.484, 57.484, 106.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 19216.732 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 276-441
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.8
Details: 9% MPD, 6% PEG 6000, 0.1M HEPES, pH 7.8, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11974 / % possible obs: 99.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.325 / % possible all: 96

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GVJ

1gvj


Resolution: 2.61→36.42 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 821361 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1232 10.3 %RANDOM
Rwork0.224 ---
obs0.224 11947 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.99 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 85.2 Å2
Baniso -1Baniso -2Baniso -3
1-10 Å20 Å20 Å2
2--10 Å20 Å2
3----20 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.61→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 0 22 2245
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.731.5
X-RAY DIFFRACTIONc_mcangle_it3.082
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 192 10.2 %
Rwork0.309 1688 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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