8HY0

Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome

Exp. Method EM
Resolution, Å 3.1
Release Date 2023-09-27
Update Date 2023-12-27
Authors Li, W., Cui, H., Lu, Z., Wang, H.
Publication PMID: 37798513
doi 10.1038/s41594-023-01121-5
RCSB PDB 8HY0
EMDB EMD-35084
Q-score 0.463
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal E canonical H3 Xenopus laevis P84233
Distal A canonical H3 Xenopus laevis P84233
H4 Proximal F canonical H4 Xenopus laevis P62799
Distal B canonical H4 Xenopus laevis P62799
H2A Proximal G canonical H2A Xenopus laevis P06897
Distal C canonical H2A Xenopus laevis P06897
H2B Proximal H canonical H2B Xenopus laevis P02281
Distal D canonical H2B Xenopus laevis P02281
Other proteins:
Chain Name UID
K Transcriptional regulatory protein SIN3 P22579
L Histone deacetylase RPD3 P32561
M Chromatin modification-related protein EAF3 Q12432
N RCO1 isoform 1 Q04779
O Chromatin modification-related protein EAF3 Q12432
P RCO1 isoform 1 Q04779
DNA:
Chain Variant Length
I 601 170
J 601 170

H3

H4

H2A

H2B

DNA

Other


Chain Bfactor Q-score Local Resolution

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.