Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.

Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M, Nat Commun 11(1):2905 (2020) Europe PMC

SASDF26 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 5.5 with 300 mM NaCl

80bp_DNA Forward
80bp_DNA Reverse
DNA-binding protein HU-alpha
MWexperimental 230 kDa
MWexpected 145 kDa
VPorod 268 nm3
log I(s) 1.53×102 1.53×101 1.53×100 1.53×10-1
80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha small angle scattering data  s, nm-1
ln I(s)
80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Guinier plot ln 1.54×102 Rg: 6.4 nm 0 (6.4 nm)-2 s2
(sRg)2I(s)/I(0)
80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot 1.104 0 3 sRg
p(r)
80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha pair distance distribution function Rg: 6.9 nm 0 Dmax: 24.4 nm

Data validation


Fits and models


log I(s)
 s, nm-1
80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha CHIMERA model

Synchrotron SAXS data from solutions of DNA-binding protein HU-alpha bound to 80 base-pair DNA in 10 mM Bis-Tris, 300 mM NaCl, pH 5.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS) storage ring (Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). 300 successive 3 second frames were collected at 10°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

80bp_DNA Forward
Mol. type   DNA
Organism   Escherichia coli
Olig. state   Monomer
Mon. MW   24.8 kDa
Sequence   FASTA
 
80bp_DNA Reverse
Mol. type   DNA
Organism   Escherichia coli
Olig. state   Monomer
Mon. MW   24.6 kDa
Sequence   FASTA
 
DNA-binding protein HU-alpha
Mol. type   Protein
Organism   Escherichia coli
Olig. state   Decamer
Mon. MW   9.5 kDa
 
UniProt   P0ACF0 (1-90)
Sequence   FASTA