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

Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD, Nucleic Acids Res 46(10):4978-4990 (2018) PubMed

SASDCW6 – Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP

Chromodomain-helicase-DNA-binding protein 1
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 373 kDa
log I(s) 2.16×10-2 2.16×10-3 2.16×10-4 2.16×10-5
Chromodomain-helicase-DNA-binding protein 1 169 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)
Chromodomain-helicase-DNA-binding protein 1 169 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: 5.6 nm 0 (5.6 nm)-2 s2
(sRg)2I(s)/I(0)
Chromodomain-helicase-DNA-binding protein 1 169 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)
Chromodomain-helicase-DNA-binding protein 1 169 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: 5.5 nm 0 Dmax: 16.7 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP Rg histogram Rg, nm
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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
Chromodomain-helicase-DNA-binding protein 1 169 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 Chd1-12N12, chromatin remodeler--nucleosome complex, in 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, 0.5 mM AMP-PNP, 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 1.88 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 nucleosomes in the presence of the chromatin remodeler Chd1 in 60% sucrose and AMP-PNP. The complex formed contains two Chd1 proteins bound to each nucleosome. Due to contrast matching between the solvent and histone proteins, the measured signal is dominated by the DNA component. The models were generated using 3D-DART and custom scripts written in Pymol. The percentage-weighting of each model in the ensemble ('XXXperc') is noted in the following model key/list that sequentially corresponds to models displayed in this entry ordered from top-to-bottom: -------------------------------------------------------------------------------------------------------- --------------SASDCW6_fit1_model1=Chd1_12N12_AMP_01_wrapped_25perc; --------------SASDCW6_fit1_model2=Chd1_12N12_AMP_02_wrapped_01perc; --------------SASDCW6_fit1_model3=Chd1_12N12_AMP_03_wrapped_01perc; --------------SASDCW6_fit1_model4=Chd1_12N12_AMP_04_extreme_02perc; --------------SASDCW6_fit1_model5=Chd1_12N12_AMP_05_extreme_01perc; --------------SASDCW6_fit1_model6=Chd1_12N12_AMP_06_inplane_01perc; --------------SASDCW6_fit1_model7=Chd1_12N12_AMP_07_inplane_11perc; --------------SASDCW6_fit1_model8=Chd1_12N12_AMP_08_inplane_08perc; --------------SASDCW6_fit1_model9=Chd1_12N12_AMP_09_inplane_03perc; --------------SASDCW6_fit1_model10=Chd1_12N12_AMP_10_inplane_12perc; --------------SASDCW6_fit1_model11=Chd1_12N12_AMP_11_inplane_01perc; --------------SASDCW6_fit1_model12=Chd1_12N12_AMP_12_inplane_03perc_dyadfliip; --------------SASDCW6_fit1_model13=Chd1_12N12_AMP_13_inplane_12perc_dyadflip; --------------SASDCW6_fit1_model14=Chd1_12N12_AMP_14_inplane_01perc_dyadflip; --------------SASDCW6_fit1_model15=Chd1_12N12_AMP_15_inplane_01perc_dyadflip; --------------SASDCW6_fit1_model16=Chd1_12N12_AMP_16_inplane_15perc; --------------SASDCW6_fit1_model17=Chd1_12N12_AMP_17_inplane_02perc.

Chromodomain-helicase-DNA-binding protein 1 (Chd1)
Mol. type   Protein
Organism   Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Olig. state   Monomers
Mon. MW   133.1 kDa
 
UniProt   P32657 (118-1274)
Sequence   FASTA
 
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