8WH5

Structure of DDM1-nucleosome complex in the apo state

Exp. Method EM
Resolution, Å 3.58
Release Date 2024-04-17
Update Date 2024-04-17
Authors Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J.
Publication PMID: 38413824
doi 10.1038/s41477-024-01640-z
RCSB PDB 8WH5
EMDB EMD-37529
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal E canonical H3 Arabidopsis thaliana P59226
Distal A canonical H3 Arabidopsis thaliana P59226
H4 Proximal B canonical H4 Arabidopsis thaliana P59259
Distal F canonical H4 Arabidopsis thaliana P59259
H2A Proximal G canonical H2A Arabidopsis thaliana Q9LD28
Distal C canonical H2A Arabidopsis thaliana Q9LD28
H2B Proximal H canonical H2B Arabidopsis thaliana O23629
Distal D canonical H2B Arabidopsis thaliana O23629
Other proteins:
Chain Name UID
K ATP-dependent DNA helicase DDM1 Q9XFH4
DNA:
Chain Variant Length
I 601 133
J 601 133

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.