7UX9

Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)

Exp. Method EM
Resolution, Å 3.2
Release Date 2023-08-09
Update Date 2023-09-27
Authors Lee, S.C., Adams, D.W., Ipsaro, J.J., Cahn, J., Lynn, J., Kim, H.S., Berube, B., Major, V., Calarco, J.P., LeBlanc, C., Bhattacharjee, S., Ramu, U., Grimanelli, D., Jacob, Y., Voigt, P., Joshua-Tor, L., Martienssen, R.A.
Publication PMID: 37643610
doi 10.1016/j.cell.2023.08.001
RCSB PDB 7UX9
EMDB EMD-26855
Q-score 0.445
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal F canonical H3 Arabidopsis thaliana P59169
Distal E canonical H3 Arabidopsis thaliana P59169
H4 Proximal H canonical H4 Xenopus laevis P62799
Distal G canonical H4 Xenopus laevis P62799
H2A Proximal B H2A.W Arabidopsis thaliana Q9FJE8
Distal A H2A.W Arabidopsis thaliana Q9FJE8
H2B Proximal D canonical H2B Arabidopsis thaliana O23629
Distal C canonical H2B Arabidopsis thaliana O23629
Other proteins:
Chain Name UID
P ATP-dependent DNA helicase DDM1 Q9XFH4
DNA:
Chain Variant Length
Y 601 141
Z 601 141

H3

H4

H2A

H2B

DNA

Other


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.