The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome

Tokuda J, Ren R, Levendosky R, Tay R, Yan M, Pollack L, Bowman G, Nucleic Acids Research (2018) DOI

SASDCT6 – 12N12 nucleosome in 60% sucrose with ADP-BeF3

169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)
Histone H2A type 1
Histone H2B 1.1
Histone H3.2
Histone H4
MWexperimental 105 kDa
MWexpected 107 kDa
log I(s) 2.16×10-2 2.16×10-3 2.16×10-4 2.16×10-5
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) Histone H2A type 1 Histone H2B 1.1 Histone H3.2 Histone H4 small angle scattering data  s, nm-1
ln I(s)
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) Histone H2A type 1 Histone H2B 1.1 Histone H3.2 Histone H4 Guinier plot ln 2.16×10-2 Rg: 4.8 nm 0 (4.8 nm)-2 s2
(sRg)2I(s)/I(0)
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) Histone H2A type 1 Histone H2B 1.1 Histone H3.2 Histone H4 Kratky plot 1.104 0 √3 sRg
p(r)
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) Histone H2A type 1 Histone H2B 1.1 Histone H3.2 Histone H4 pair distance distribution function Rg: 4.9 nm 0 Dmax: 14 nm

Experimental data validation

Fits and models

log I(s)
 s, nm-1
12N12 nucleosome in 60% sucrose with ADP-BeF3 Rg histogram Rg, nm
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) Histone H2A type 1 Histone H2B 1.1 Histone H3.2 Histone H4 CUSTOM IN-HOUSE model
Synchrotron SAXS data from solutions of 12N12 nucleosome in 60% sucrose with ADP-BeF3 in 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, ADP-BeF3 (0.5 mM ADP, 4 mM NaF, 0.6 mM BeCl2), pH 7.8, were collected on the G1 beam line at the Cornell High Energy Synchrotron Source (Ithaca, NY, USA) using a Pilatus Pilatus 200K detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1109 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 1.10 mg/ml was measured at 25°C. 40 successive 10 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 to produce the scattering profile displayed in this entry.

12N12 nucleosome measured in 60% sucrose and ADP-BeF3. Due to contrast matching between the solvent and histone proteins (due to sucrose), the measured signal is dominated by the DNA component. The model was generated using 3D-DART and custom scripts written in Pymol. The percentage-weighting of each model in the ensemble ('XXXperc') is noted in the model key below: SASDCT6_fit1_model1 = 12N12_ADP_01_100perc

169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) (DNA)
Mol. type   DNA
Olig. state   Monomer
Mon. MW   52.5 kDa
Sequence   FASTA
 
Histone H2A type 1 (H2A)
Mol. type   Protein
Organism   Xenopus laevis
Olig. state   Monomer
Mon. MW   14.0 kDa
 
UniProt   P06897
Sequence   FASTA
 
Histone H2B 1.1 (H2B)
Mol. type   Protein
Organism   Xenopus laevis
Olig. state   Monomer
Mon. MW   13.9 kDa
 
UniProt   P02281
Sequence   FASTA
 
Histone H3.2 (H3)
Mol. type   Protein
Organism   Xenopus laevis
Olig. state   Monomer
Mon. MW   15.4 kDa
 
UniProt   P84233
Sequence   FASTA
 
Histone H4 (H4)
Mol. type   Protein
Organism   Xenopus laevis
Olig. state   Monomer
Mon. MW   11.4 kDa
 
UniProt   P62799
Sequence   FASTA