8XBT

The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding

Exp. Method	EM
Resolution, Å	4.12
Release Date	2024-03-27
Update Date	2024-05-08
Authors	Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H.
Publication	PMID: 38509361
doi	10.1038/s41586-024-07196-4
RCSB PDB	8XBT
EMDB	EMD-38228
Q-score	0.199

Core histones in Nucleosome-like particles:

	Side	Chain	HistoneDB Variant	Taxa	UID
H3	Proximal	E	canonical H3	Homo sapiens	P68431
H3	Distal	A	canonical H3	Homo sapiens	P68431
H4	Proximal	F	canonical H4	Homo sapiens	P62805
H4	Distal	B	canonical H4	Homo sapiens	P62805
H2A	Proximal	G	canonical H2A	Homo sapiens	P04908
H2A	Distal	C	canonical H2A	Homo sapiens	P04908
H2B	Proximal	H	canonical H2B	Homo sapiens	P06899
H2B	Distal	D	canonical H2B	Homo sapiens	P06899

Other proteins:

Chain	Name	UID
K	DNA repair protein RAD51 homolog 1	Q06609
L	DNA repair protein RAD51 homolog 1	Q06609
M	DNA repair protein RAD51 homolog 1	Q06609
N	DNA repair protein RAD51 homolog 1	Q06609
O	DNA repair protein RAD51 homolog 1	Q06609
P	DNA repair protein RAD51 homolog 1	Q06609
Q	DNA repair protein RAD51 homolog 1	Q06609
R	DNA repair protein RAD51 homolog 1	Q06609

DNA:

Chain	Variant	Length
I	601_modified	156
J	601_modified	153

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 A

H4d chain B

H2Ad chain C

H2Bd chain D

H3p chain E

H4p chain F

H2Ap chain G

H2Bp chain H

DNA top chain I, bot chain J

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