8IHT

Rpd3S bound to the nucleosome

Exp. Method EM
Resolution, Å 3.72
Release Date 2024-03-20
Update Date 2024-03-20
Authors Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X.
Publication PMID: 37845487
doi 10.1038/s41422-023-00884-2
RCSB PDB 8IHT
EMDB EMD-35455
Q-score 0.345
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal A canonical H3 Xenopus laevis A0A310TTQ1
Distal E canonical H3 Xenopus laevis A0A310TTQ1
H4 Proximal B canonical H4 Xenopus laevis A0A8J1LTD2
Distal F canonical H4 Xenopus laevis A0A8J1LTD2
H2A Proximal C canonical H2A Xenopus laevis Q6AZJ8
Distal G canonical H2A Xenopus laevis Q6AZJ8
H2B Proximal D canonical H2B Xenopus laevis A0A8J0U496
Distal H canonical H2B Xenopus laevis A0A8J0U496
Other proteins:
Chain Name UID
K Transcriptional regulatory protein SIN3 P22579
L Histone deacetylase RPD3 P32561
M RCO1 isoform 1 A0A8H4BXB0
N Chromatin modification-related protein EAF3 A0A8H4F719
O RCO1 isoform 1 A0A8H4BXB0
P Chromatin modification-related protein EAF3 A0A8H4F719
DNA:
Chain Variant Length
I 601 158
J 601 159

H3

H4

H2A

H2B

DNA

Other


Chain Bfactor Q-score

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.