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- PDB-6da1: ETS1 in complex with synthetic SRR mimic -

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Basic information

Entry
Database: PDB / ID: 6da1
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 / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding ...Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / DNA-binding transcription factor activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA 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: 2.0001269892 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 1, 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: serine-rich region (SRR) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2346
Polymers34,9463
Non-polymers2883
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-61 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.330, 75.330, 115.331
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 16268.591 Da / Num. of mol.: 2
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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.76 Å3/Da / Density % sol: 55.42 % / Description: cubic
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: PEG 3350, lithium sulfate, ethylene glycol, MES / PH range: 7.0-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97952 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2→65.24 Å / Num. obs: 26181 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 41.0002441188 Å2 / CC1/2: 0.999 / R split: 0.04 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.038 / Rrim(I) all: 0.094 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.898 / CC1/2: 0.938 / Rpim(I) all: 0.55

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Processing

Software
NameVersionClassification
MxDCdata collection
AutoProcessdata extraction
MOSFLM7.2.2data reduction
Aimless0.5.32data scaling
TRUNCATE1.17.25data processing
PHASER2.8.0phasing
Coot0.8.9model building
PHENIX1.12_2829refinement
Aimlessdata scaling
Aimlessdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MD0

1md0


Resolution: 2.0001269892→56.7828354451 Å / SU ML: 0.235777847374 / Cross valid method: FREE R-VALUE / σ(F): 1.33645593417 / Phase error: 27.1600854185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247799228588 1311 5.00993579945 %
Rwork0.215791645135 24857 -
obs0.217423045467 26168 99.9236291431 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.1587261361 Å2
Refinement stepCycle: LAST / Resolution: 2.0001269892→56.7828354451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 15 161 2584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017212045862503
X-RAY DIFFRACTIONf_angle_d0.440850200613402
X-RAY DIFFRACTIONf_chiral_restr0.0353160713619338
X-RAY DIFFRACTIONf_plane_restr0.00188770981477426
X-RAY DIFFRACTIONf_dihedral_angle_d7.27312249031461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.08020.3575208945651270.3238640154472724X-RAY DIFFRACTION100
2.0802-2.17490.2782830805591570.2870561876852720X-RAY DIFFRACTION99.8611593197
2.1749-2.28960.2901858485361240.2478701253782741X-RAY DIFFRACTION99.9302406697
2.2896-2.4330.2796658830441590.2483352821192704X-RAY DIFFRACTION99.9650837989
2.433-2.62090.2752056062981200.2351081621222767X-RAY DIFFRACTION99.9653739612
2.6209-2.88460.2767899744311630.2366258832062733X-RAY DIFFRACTION99.9309868875
2.8846-3.3020.2721744591471400.2261579408412761X-RAY DIFFRACTION100
3.302-4.15990.2268196933111700.1912895680052783X-RAY DIFFRACTION99.9661475965
4.1599-56.80570.2227020123211510.1942421038922924X-RAY DIFFRACTION99.7405124878
Refinement TLS params.Method: refined / Origin x: 35.9793539016 Å / Origin y: 38.0181356515 Å / Origin z: 28.9284815153 Å
111213212223313233
T0.259167175316 Å20.0532921436964 Å2-0.0193855103678 Å2-0.446488249937 Å20.0209318801424 Å2--0.402941924304 Å2
L2.94990560633 °20.545038229318 °20.537137981037 °2-0.941306443849 °2-0.30367354485 °2--2.58575403035 °2
S-0.000786463133211 Å °0.137314385767 Å °0.141686855102 Å °0.0709771148541 Å °-0.0164016616684 Å °0.0469487193627 Å °-0.231116762604 Å °-0.26625247459 Å °0.0159979051085 Å °
Refinement TLS groupSelection details: all

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