The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding

Bernardini A, Lorenzo M, Chaves-Sanjuan A, Swuec P, Pigni M, Saad D, Konarev P, Graewert M, Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N, International Journal of Biological Macromolecules (2021) DOI

SASDKW9 – Transcription factors USF1 and NF-Y bound to a CCAAT DNA box(50bp)

Upstream stimulatory factor 1
Nuclear transcription factor Y subunit alpha
Nuclear transcription factor Y subunit beta
Nuclear transcription factor Y subunit gamma
DNA 50bp
MWI(0) 104 kDa
MWexpected 112 kDa
VPorod 165 nm3
log I(s) 2.97×104 2.97×103 2.97×102 2.97×101
Upstream stimulatory factor 1 Nuclear transcription factor Y subunit alpha Nuclear transcription factor Y subunit beta Nuclear transcription factor Y subunit gamma DNA 50bp small angle scattering data  s, nm-1
ln I(s)
Upstream stimulatory factor 1 Nuclear transcription factor Y subunit alpha Nuclear transcription factor Y subunit beta Nuclear transcription factor Y subunit gamma DNA 50bp Guinier plot ln 2.98×104 Rg: 4.8 nm 0 (4.8 nm)-2 s2
(sRg)2I(s)/I(0)
Upstream stimulatory factor 1 Nuclear transcription factor Y subunit alpha Nuclear transcription factor Y subunit beta Nuclear transcription factor Y subunit gamma DNA 50bp Kratky plot 1.104 0 3 sRg
p(r)
Upstream stimulatory factor 1 Nuclear transcription factor Y subunit alpha Nuclear transcription factor Y subunit beta Nuclear transcription factor Y subunit gamma DNA 50bp pair distance distribution function Rg: 4.9 nm 0 Dmax: 17 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Upstream stimulatory factor 1 Nuclear transcription factor Y subunit alpha Nuclear transcription factor Y subunit beta Nuclear transcription factor Y subunit gamma DNA 50bp DAMMIN model

log I(s)
 s, nm-1
Upstream stimulatory factor 1 Nuclear transcription factor Y subunit alpha Nuclear transcription factor Y subunit beta Nuclear transcription factor Y subunit gamma DNA 50bp CORAL model

Synchrotron SAXS data from solutions of transcription factors USF1 and NF-Y bound to a 50 base pair CCAAT DNA box in 100 mM cacodylate buffer, pH 6.5 were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 1.00 mg/ml was measured at 15°C. 20 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Upstream stimulatory factor 1 (USF1)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   25.0 kDa
 
UniProt   P22415 (106-310)
Sequence   FASTA
 
Nuclear transcription factor Y subunit alpha (NF-Y A)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   9.5 kDa
 
UniProt   P23511 (262-332)
Sequence   FASTA
 
Nuclear transcription factor Y subunit beta (NF-Y B)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   10.6 kDa
 
UniProt   P25208 (52-143)
Sequence   FASTA
 
Nuclear transcription factor Y subunit gamma (NF-Y C)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   11.1 kDa
 
UniProt   Q13952 (27-120)
Sequence   FASTA
 
DNA 50bp (DNA50bp)
Mol. type   DNA
Olig. state   Monomer
Mon. MW   30.9 kDa
Sequence   FASTA