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 Oct)

doi: 10.1016/j.ijbiomac.2021.10.056 		Submitted to SASBDB: 2021 Mar 5
Published in SASBDB:

SASDKV9 – Transcription factors USF1 and NF-Y bound to a CCAAT DNA box(48bp)

Upstream stimulatory factor 1Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 48bp experimental SAS data
CORAL model
Sample: Upstream stimulatory factor 1 dimer, 50 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 48bp monomer, 30 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Jun 14
RgGuinier 4.8 nm
Dmax 17.0 nm
VolumePorod 155 nm3

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

Upstream stimulatory factor 1Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 50bp experimental SAS data
DAMMIN model
Sample: Upstream stimulatory factor 1 dimer, 50 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 50bp monomer, 31 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Jun 14
RgGuinier 4.8 nm
Dmax 17.0 nm
VolumePorod 165 nm3

SASDKX9 – Transcription factors MAX and NF-Y bound to a CCAAT DNA box(48bp)

Protein max (Isoform 2, short, 13-21: missing)Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 48bp experimental SAS data
DAMMIN model
Sample: Protein max (Isoform 2, short, 13-21: missing) dimer, 39 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 48bp monomer, 30 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2012 Dec 10
RgGuinier 5.2 nm
Dmax 17.0 nm
VolumePorod 151 nm3