8TOF

Rpd3S bound to an H3K36Cme3 modified nucleosome

Exp. Method EM
Resolution, Å 2.8
Release Date 2024-01-17
Update Date 2024-01-17
Authors Markert, J.W., Vos, S.M., Farnung, L.
Publication PMID: 38065958
doi 10.1038/s41467-023-43968-8
RCSB PDB 8TOF
EMDB EMD-41449
Q-score 0.464
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal e canonical H3 Xenopus laevis P02302
Distal a canonical H3 Xenopus laevis P02302
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
A Transcriptional regulatory protein SIN3 P22579
B Histone deacetylase RPD3 P32561
D Chromatin modification-related protein EAF3 Q12432
E Chromatin modification-related protein EAF3 Q12432
F Transcriptional regulatory protein RCO1 Q04779
G Transcriptional regulatory protein RCO1 Q04779
H Rco1 NA
x histone N-terminal tail NA
DNA:
Chain Variant Length
N 601_modified 176
T 601_modified 176

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.