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
H3	Distal	O	canonical H3	Xenopus laevis	P84233
H4	Proximal	T	canonical H4	Xenopus laevis	P62799
H4	Distal	P	canonical H4	Xenopus laevis	P62799
H2A	Proximal	U	canonical H2A	Xenopus laevis	P06897
H2A	Distal	Q	canonical H2A	Xenopus laevis	P06897
H2B	Proximal	V	canonical H2B	Xenopus laevis	P02281
H2B	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

Orthographic Superimpose 1KX5 Show axes

Aligned nucleosome coordinates

X - Y

X - Z

Z - Y

Nucleosome reference frame definition

DNA relative twist and local base step parameters

3DNA

Relative Twist

Sequence on X-axis is numbered relative to the dyad base pair.

Atomic contacts between nucleosomal entities.

H3d chain O

H4d chain P

H2Ad chain Q

H2Bd chain R

H3p chain S

H4p chain T

H2Ap chain U

H2Bp chain V

DNA top chain Y, bot chain X

Hover the mouse cursor on the barplot to show contact information. Oncogenic mutations of non-histone proteins in contact are highlighted.