A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.

Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A, Cell Rep 27(2):387-399.e7 (2019) Europe PMC

SASDFY3 – Semi-synthetic nucleosome core particle (NCP) in complex with lysine-specific demethylase (LSD2) and the dehydrogenase domain plus linker of cytokine-like nuclear factor (NPAC delta-205)

Lysyne-specific Demethylase LSD2
NPAC linker+DH (delta-205)
Histone H3
Histone H4
Histone H2a
Histone H2b
147bp 601 Widom sequence
MWexperimental 530 kDa
MWexpected 392 kDa
VPorod 1100 nm3
log I(s) 1.57×102 1.57×101 1.57×100 1.57×10-1
Lysyne-specific Demethylase LSD2 NPAC linker+DH (delta-205) Histone H3 Histone H4 Histone H2a Histone H2b 147bp 601 Widom sequence small angle scattering data  s, nm-1
ln I(s)
Lysyne-specific Demethylase LSD2 NPAC linker+DH (delta-205) Histone H3 Histone H4 Histone H2a Histone H2b 147bp 601 Widom sequence Guinier plot ln 1.58×102 Rg: 7.8 nm 0 (7.8 nm)-2 s2
(sRg)2I(s)/I(0)
Lysyne-specific Demethylase LSD2 NPAC linker+DH (delta-205) Histone H3 Histone H4 Histone H2a Histone H2b 147bp 601 Widom sequence Kratky plot 1.104 0 3 sRg
p(r)
Lysyne-specific Demethylase LSD2 NPAC linker+DH (delta-205) Histone H3 Histone H4 Histone H2a Histone H2b 147bp 601 Widom sequence pair distance distribution function Rg: 8.4 nm 0 Dmax: 30.4 nm

Data validation


There are no models related to this curve.

Synchrotron SAXS data from solutions of a semi-synthetic nucleosome core particle (NCP) in complex with lysine-specific demethylase (LSD2) and truncated cytokine-like nuclear factor (NPAC delta-205) in 15 mM HEPES, 200 mM NaCl, pH 7.3 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20 °C using the following parameters: Column: Wyatt WTC-030N5; Flow rate: 0.25 mL/min; Sample injection concentration: 3 mg/mL; Injection volume: 50 μL. The data were collected through the SEC peak of the sample as a series of 70 x 1 second exposures. Each unsubtracted data frame was normalised to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted. The resulting subtracted frames were scaled and averaged to generate the final SAXS profile displayed in this entry.

Lysyne-specific Demethylase LSD2 (LSD2)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   88.8 kDa
 
UniProt   Q8NB78 (31-822)
Sequence   FASTA
 
NPAC linker+DH (delta-205) (NPAC delta205)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Tetramer
Mon. MW   37.4 kDa
 
UniProt   Q49A26 (205-553)
Sequence   FASTA
 
Histone H3 (H3)
Mol. type   Protein
Organism   Xenopus laevis
Olig. state   Dimer
Mon. MW   15.3 kDa
Sequence   FASTA
 
Histone H4 (H4)
Mol. type   Protein
Organism   Xenopus laevis
Olig. state   Dimer
Mon. MW   11.2 kDa
 
UniProt   P62799 (2-103)
Sequence   FASTA
 
Histone H2a (H2a)
Mol. type   Protein
Organism   Xenopus laevis
Olig. state   Dimer
Mon. MW   14.0 kDa
 
UniProt   Q6AZJ8 (2-130)
Sequence   FASTA
 
Histone H2b (H2b)
Mol. type   Protein
Organism   Xenopus laevis
Olig. state   Dimer
Mon. MW   13.5 kDa
 
UniProt   Q92130 (5-126)
Sequence   FASTA
 
147bp 601 Widom sequence (601-147bp)
Mol. type   DNA
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   45.2 kDa
Sequence   FASTA