SASDAP7: PBX1-PREB1 complex (Pre-B-cell leukemia transcription factor 1, P...

Basic information

• Entry: Database: SASBDB / ID: SASDAP7

Sample

PBX1-PREB1 complex

• Pre-B-cell leukemia transcription factor 1 (protein), PBX1, Homo sapiens
• Homeobox protein PKNOX1 (protein), PREP1, Homo sapiens

Function / homology

Function:

urogenital system development / natural killer cell differentiation / proximal/distal pattern formation / embryonic skeletal system development / sex differentiation / Transcriptional regulation of pluripotent stem cells / eye development / steroid biosynthetic process / camera-type eye development / embryonic limb morphogenesis / embryonic hemopoiesis / anterior/posterior pattern specification / NOTCH3 Intracellular Domain Regulates Transcription / adrenal gland development / branching involved in ureteric bud morphogenesis / positive regulation of stem cell proliferation / T cell differentiation / negative regulation of neuron differentiation / regulation of ossification / neuron development / embryonic organ development / spleen development / positive regulation of G2/M transition of mitotic cell cycle / transcription corepressor binding / thymus development / erythrocyte differentiation / stem cell proliferation / transcription coregulator binding / animal organ morphogenesis / brain development / negative regulation of DNA-binding transcription factor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / G2/M transition of mitotic cell cycle / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm

Domain/homology:

Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / PBX, PBC domain / PBC domain / PBC domain profile. / : / Homeobox KN domain / Homeobox KN domain / Homeobox, conserved site / 'Homeobox' domain signature. / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily

Component:

Pre-B-cell leukemia transcription factor 1 / Homeobox protein PKNOX1

• Biological species: Homo sapiens (human)
• 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 #288: ; Type: dummy / Software: DAMMIF / Radius of dummy atoms: 4.00 A / Chi-square value: 1.340964; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: PBX1-PREB1 complex / Specimen concentration: 1.50-2.80 / Entity id: 160 / 161
• Buffer: Name: Tris-HCl / Concentration: 20.00 mM / pH: 7.4 / Composition: 150 mM NaCl, 5% glycerol, 1 mM DTT

Entity #160

Name: PBX1 / Type: protein / Description: Pre-B-cell leukemia transcription factor 1 / Formula weight: 34.455 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P40424
Sequence:

MDEQPRLMHS HAGVGMAGHP GLSQHLQDGA GGTEGEGGRK QDIGDILQQI MTITDQSLDE AQARKHALNC HRMKPALFNV LCEIKEKTVL SIRGAQEEEP TDPQLMRLDN MLLAEGVAGP EKGGGSAAAA AAAAASGGAG SDNSVEHSDY RAKLSQIRQI YHTELEKYEQ ACNEFTTHVM NLLREQSRTR PISPKEIERM VSIIHRKFSS IQMQLKQSTC EAVMILRSRF LDARRKRRNF NKQATEILNE YFYSHLSNPY PSEEAKEELA KKCGITVSQV SNWFGNKRIR YKKNIGKFQE EANIYAAK

Entity #161

Name: PREP1 / Type: protein / Description: Homeobox protein PKNOX1 / Formula weight: 38.339 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P55347
Sequence:

MMATQTLSID SYQDGQQMQV VTELKTEQDP NCSEPDAEGV SPPPVESQTP MDVDKQAIYR HPLFPLLALL FEKCEQSTQG SEGTTSASFD VDIENFVRKQ EKEGKPFFCE DPETDNLMVK AIQVLRIHLL ELEKVNELCK DFCSRYIACL KTEMNSETLL SGEPGSPYSP VQSQQIQSAI TGTISPQGIV VPASALQQGN VAMATVAGGT VYQPVTVVTP QGQVVTQTLS PGTIRIQNSQ LQLQLNQDLS ILHQDDGSSK NKRGVLPKHA TNVMRSWLFQ HIGHPYPTED EKKQIAAQTN LTLLQVNNWF INARRRILQP MLDSSCSETP KTKKKTAQNR PVQRF

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: The complex between the homeodomain proteins PREP1 / Measurement date: Dec 6, 2013 / Exposure time: 0.05 sec. / Number of frames: 50 / Unit: 1/nm /

	Min	Max
Q	0.0275	4.4504

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 462 /

	Min	Max
Q	0.1275	1.34
P(R) point	38	499
R	0	19

Result

Type of curve: merged

	Experimental	Standard	Porod
MW	77 kDa	77 kDa	84 kDa
Volume	-	-	143 nm3

	P(R)	Guinier
Forward scattering, I0	1580	1580.53
Radius of gyration, Rg	5.7 nm	5.846 nm

	Min	Max
D	-	19
Guinier point	29	75