6VYP

Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate

Exp. Method X-ray
Resolution, Å 4.99
Release Date 2020-05-27
Update Date 2023-10-11
Authors Kim, S.A., Zhu, J., Yennawar, N., Eek, P., Tan, S.
Publication PMID: 32396821
doi 10.1016/j.molcel.2020.04.019
RCSB PDB 6VYP
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal A canonical H3 Xenopus laevis P84233
Distal E canonical H3 Xenopus laevis P84233
H4 Proximal B canonical H4 Xenopus laevis P62799
Distal F canonical H4 Xenopus laevis P62799
H2A Proximal C canonical H2A Xenopus laevis P06897
Distal G canonical H2A Xenopus laevis P06897
H2B Proximal D canonical H2B Xenopus laevis P02281
Distal H canonical H2B Xenopus laevis P02281
Other proteins:
Chain Name UID
K Lysine-specific histone demethylase 1A O60341
L REST corepressor 1 Q9UKL0
M Lysine-specific histone demethylase 1A O60341
N REST corepressor 1 Q9UKL0
k Lysine-specific histone demethylase 1A O60341
l REST corepressor 1 Q9UKL0
m Lysine-specific histone demethylase 1A O60341
n REST corepressor 1 Q9UKL0
DNA:
Chain Variant Length
I 601 191
J 601 191
i 601 191
j 601 191

H3

H4

H2A

H2B

DNA

Other


Chain Bfactor

Aligned nucleosome coordinates

Nucleosome reference frame definition

DNA relative twist and local base step parameters

Sequence on X-axis is numbered relative to the dyad base pair.

Atomic contacts between nucleosomal entities.


Hover the mouse cursor on the barplot to show contact information. Oncogenic mutations of non-histone proteins in contact are highlighted.