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- PDB-6dat: ETS1 in complex with synthetic SRR mimic -

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Basic information

Entry
Database: PDB / ID: 6dat
TitleETS1 in complex with synthetic SRR mimic
Components
  • Protein C-ets-1
  • serine-rich region (SRR) peptide
KeywordsDNA BINDING PROTEIN / ETS1 / transcription factor / complex / autoinhibition
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
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35002638783 Å
AuthorsPerez-Borrajero, C. / Okon, M. / Lin, C.S. / Scheu, K. / Murphy, M.E.P. / Graves, B.J. / McIntosh, L.P.
Citation
Journal: J. Mol. Biol. / Year: 2019
Title: The Biophysical Basis for Phosphorylation-Enhanced DNA-Binding Autoinhibition of the ETS1 Transcription Factor.
Authors: Perez-Borrajero, C. / Lin, C.S. / Okon, M. / Scheu, K. / Graves, B.J. / Murphy, M.E.P. / McIntosh, L.P.
#1: Journal: J. Appl. Crystallogr. / Year: 2007
Title: Phaser crystallographic software
Authors: McCoy, A.J. / Grosse-Kunstleve, R.W.
History
DepositionMay 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Oct 4, 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: Protein C-ets-1
D: Protein C-ets-1
E: serine-rich region (SRR) peptide
F: serine-rich region (SRR) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,75615
Polymers69,8926
Non-polymers8659
Water1,11762
1
A: Protein C-ets-1
B: Protein C-ets-1
F: serine-rich region (SRR) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4268
Polymers34,9463
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein C-ets-1
D: Protein C-ets-1
E: serine-rich region (SRR) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3307
Polymers34,9463
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.111, 89.111, 215.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 16268.591 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ets1, Ets-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P27577
#2: Protein/peptide serine-rich region (SRR) peptide


Mass: 2408.770 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: MES, PEG 3350, lithium sulfate / PH range: 8.5-9.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.35→39.19 Å / Num. obs: 37109 / % possible obs: 99.8 % / Redundancy: 13 % / Biso Wilson estimate: 41.3150443825 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.038 / Net I/σ(I): 12.8
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 1.898 / Num. unique all: 754 / Num. unique obs: 8714 / CC1/2: 0.938 / Rpim(I) all: 0.55

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Processing

Software
NameVersionClassification
Web-Icedata collection
XDSdata reduction
PHASER2.8.0phasing
Coot0.8.9model building
PHENIX1.12_2829refinement
Aimlessdata scaling
Aimlessdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DA1

6da1


Resolution: 2.35002638783→39.1884261038 Å / SU ML: 0.331559828187 / Cross valid method: FREE R-VALUE / σ(F): 1.33390682013 / Phase error: 36.1255414302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.268011974826 1973 5.38997404726 %
Rwork0.232859474543 34632 -
obs0.234759949156 36605 98.6657681941 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.9959072805 Å2
Refinement stepCycle: LAST / Resolution: 2.35002638783→39.1884261038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 0 45 62 4859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002810581320234918
X-RAY DIFFRACTIONf_angle_d0.5062469117166678
X-RAY DIFFRACTIONf_chiral_restr0.0363718766967662
X-RAY DIFFRACTIONf_plane_restr0.00224434133969826
X-RAY DIFFRACTIONf_dihedral_angle_d10.82115476182846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40880.4515958928341370.4089042739042410X-RAY DIFFRACTION98.1124807396
2.4088-2.47390.3967432447511340.3684490791712398X-RAY DIFFRACTION97.4220854175
2.4739-2.54670.383177301481380.3363774111092407X-RAY DIFFRACTION98.4526112186
2.5467-2.62890.3701107489051380.3025759939162435X-RAY DIFFRACTION98.2061068702
2.6289-2.72280.3605917456531360.3043814217352413X-RAY DIFFRACTION98.8367584335
2.7228-2.83180.3851749050871390.2925521389932422X-RAY DIFFRACTION98.2355197545
2.8318-2.96060.3125555856671390.2792078766162464X-RAY DIFFRACTION98.5238455715
2.9606-3.11670.3369858068791380.295626457922430X-RAY DIFFRACTION98.1651376147
3.1167-3.31180.3620455820321430.2709274252732462X-RAY DIFFRACTION98.5249621785
3.3118-3.56740.2375860236851410.220145210252480X-RAY DIFFRACTION99.0177559501
3.5674-3.92610.2368304700291430.2005724731232498X-RAY DIFFRACTION99.5101733233
3.9261-4.49350.206869253991460.1820753871372551X-RAY DIFFRACTION99.8519067012
4.4935-5.65860.2035917262281460.1844080410962545X-RAY DIFFRACTION99.1525423729
5.6586-39.19390.2191882310661550.2003535054042717X-RAY DIFFRACTION99.2055267703

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