SASDAR7: DNA 22mer

Basic information

• Entry: Database: SASBDB / ID: SASDAR7

Sample

DNA 22mer

• DNA 22mer (DNA)

• Citation: Journal: FEBS J / Year: 2016; Title: The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding.; Authors: Lisa Mathiasen / Erica Valentini / Stephane Boivin / Angela Cattaneo / Francesco Blasi / Dmitri I Svergun / Chiara Bruckmann / ; Abstract: Transcription factors are known to modify the DNA that they bind. However, DNA can also serve as an allosteric ligand whose binding modifies the conformation of transcriptional regulators. Here, we describe how heterodimer PBX1:PREP1, formed by proteins playing major roles in embryonic development and tumorigenesis, undergoes an allosteric transition upon DNA binding. We demonstrate through a number of biochemical and biophysical methods that PBX1:PREP1 exhibits a structural change upon DNA binding. Small-angle X-ray scattering (SAXS), circular dichroism (CD), isothermal titration calorimetry (ITC), and limited proteolysis demonstrate a different shape, α-helical content, thermodynamic behavior, and solution environment of the holo-complex (with DNA) compared to the apo-complex (without DNA). Given that PBX1 as such does not have a defined DNA selectivity, structural changes upon DNA binding become major factors in the function of the PBX1:PREP1 complex. The observed changes are mapped at both the amino- and carboxy-terminal regions of the two proteins thereby providing important insights to determine how PBX1:PREP1 dimer functions.; DATABASE: Small-angle scattering data are available in SASBDB under accession numbers SASDAP7, SASDAQ7, and SASDAR7.

Contact author

• Erica Valentini (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #293: ; Type: dummy / Software: DAMMIF / Radius of dummy atoms: 1.50 A / Chi-square value: 1.056784; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: DNA 22mer / Specimen concentration: 1.50-1.50
• Buffer: Name: Tris-HCl / Concentration: 20.00 mM / pH: 7.4 / Composition: 150 mM NaCl, 5% glycerol, 1 mM DTT

Entity #162

Type: DNA / Description: DNA 22mer / Formula weight: 11.9 / Num. of mol.: 1
Sequence:

5GCCTAGTGA TTGACAGATT CCT3

Experimental information

• Beam: Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: DNA / Measurement date: Dec 6, 2013 / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.2222	4.4504

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 387 /

	Min	Max
Q	0.138	3.182
P(R) point	42	428
R	0	7.5

Result

D max: 7.5 / Type of curve: single_conc /

	Experimental	Porod
MW	13 kDa	19 kDa
Volume	-	19 nm3

	P(R)	Guinier
Forward scattering, I0	1277	1260
Radius of gyration, Rg	2.3 nm	2.2 nm