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- PDB-4bqa: Crystal structure of the ETS domain of human ETS2 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 4bqa
TitleCrystal structure of the ETS domain of human ETS2 in complex with DNA
Components
  • 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
  • 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'
  • PROTEIN C-ETS-2
KeywordsTRANSCRIPTION / TRANSCRIPTIONAL REGULATOR / DNA COMPLEX
Function / homology
Function and homology information


ectodermal cell fate commitment / primitive streak formation / nuclear glucocorticoid receptor binding / mesoderm development / skeletal system development / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...ectodermal cell fate commitment / primitive streak formation / nuclear glucocorticoid receptor binding / mesoderm development / skeletal system development / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Transforming protein C-ets-2 / 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 ...Transforming protein C-ets-2 / 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 / Protein C-ets-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNewman, J.A. / Cooper, C.D.O. / Krojer, T. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Gileadi, O.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Insights Into the Autoregulation and Cooperativity of the Human Transcription Factor Ets-2.
Authors: Newman, J.A. / Cooper, C.D.O. / Aitkenhead, H. / Gileadi, O.
History
DepositionMay 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN C-ETS-2
B: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
C: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'
D: PROTEIN C-ETS-2
E: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
F: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'
G: PROTEIN C-ETS-2
H: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
I: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)67,6119
Polymers67,6119
Non-polymers00
Water59433
1
A: PROTEIN C-ETS-2
B: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
C: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers22,5373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-18.7 kcal/mol
Surface area9370 Å2
MethodPISA
2
G: PROTEIN C-ETS-2
H: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
I: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers22,5373
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-20 kcal/mol
Surface area7570 Å2
MethodPISA
3
D: PROTEIN C-ETS-2
E: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
F: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers22,5373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-19.3 kcal/mol
Surface area7340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.674, 96.964, 83.803
Angle α, β, γ (deg.)90.00, 97.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN C-ETS-2


Mass: 16446.861 Da / Num. of mol.: 3 / Fragment: ETS DOMAIN, RESIDUES 325-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15036
#2: DNA chain 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'


Mass: 3094.042 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: DNA chain 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'


Mass: 2995.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 2 RESIDUES REMAIN AFTER TEV CLEAVAGE OF HIS TAG

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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: 2.19 Å3/Da / Density % sol: 43.76 % / Description: NONE
Crystal growDetails: 0.1 M BIS TRIS PH 5.5, 0.25 M NACL, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→48.5 Å / Num. obs: 20136 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 63.45 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.62 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZP5

3zp5


Resolution: 2.5→48.482 Å / SU ML: 0.35 / σ(F): 0.01 / Phase error: 32.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 1966 5.1 %
Rwork0.2339 --
obs0.2349 19601 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 1212 0 33 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033935
X-RAY DIFFRACTIONf_angle_d0.7895577
X-RAY DIFFRACTIONf_dihedral_angle_d20.7431516
X-RAY DIFFRACTIONf_chiral_restr0.041581
X-RAY DIFFRACTIONf_plane_restr0.002504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56260.33831410.32452244X-RAY DIFFRACTION84
2.5626-2.63190.37251390.31362443X-RAY DIFFRACTION91
2.6319-2.70940.35261700.30862505X-RAY DIFFRACTION96
2.7094-2.79680.35281430.3012674X-RAY DIFFRACTION98
2.7968-2.89680.26591190.29762691X-RAY DIFFRACTION99
2.8968-3.01270.36531290.27972672X-RAY DIFFRACTION100
3.0127-3.14980.26311360.25872638X-RAY DIFFRACTION98
3.1498-3.31590.32681380.25522624X-RAY DIFFRACTION96
3.3159-3.52350.3031180.25442521X-RAY DIFFRACTION95
3.5235-3.79550.26051330.22252699X-RAY DIFFRACTION99
3.7955-4.17730.22351420.21242707X-RAY DIFFRACTION100
4.1773-4.78130.19521450.19582638X-RAY DIFFRACTION99
4.7813-6.02210.21341770.20682658X-RAY DIFFRACTION100
6.0221-48.49110.26271360.23292679X-RAY DIFFRACTION99

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