8KD2

Rpd3S in complex with 187bp nucleosome

Exp. Method EM
Resolution, Å 3.02
Release Date 2023-09-13
Update Date 2023-10-11
Authors Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J.
Publication PMID: 37666978
doi 10.1038/s41422-023-00869-1
RCSB PDB 8KD2
EMDB EMD-37122
Q-score 0.35
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal S canonical H3 Xenopus laevis P84233
Distal O canonical H3 Xenopus laevis P84233
H4 Proximal T canonical H4 Xenopus laevis P62799
Distal P canonical H4 Xenopus laevis P62799
H2A Proximal U canonical H2A Xenopus laevis P06897
Distal Q canonical H2A Xenopus laevis P06897
H2B Proximal V canonical H2B Xenopus laevis P02281
Distal R canonical H2B Xenopus laevis P02281
Other proteins:
Chain Name UID
A Histone deacetylase RPD3 P32561
B Transcriptional regulatory protein SIN3 P22579
D Chromatin modification-related protein EAF3 Q12432
E Transcriptional regulatory protein RCO1 Q04779
F Chromatin modification-related protein EAF3 Q12432
G Transcriptional regulatory protein RCO1 Q04779
DNA:
Chain Variant Length
X 601 174
Y 601 174

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.