8BZ1

RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W)

Exp. Method	EM
Resolution, Å	3.8
Release Date	2023-05-03
Update Date	2023-06-14
Authors	Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P.
Publication	PMID: 37148879
doi	10.1016/j.molcel.2023.04.011
Related structures	8BYQ, 8BVW
RCSB PDB	8BZ1
EMDB	EMD-16335
Q-score	0.244

Core histones in Nucleosome-like particles:

	Side	Chain	HistoneDB Variant	Taxa	UID
H3	Proximal	a	canonical H3	Xenopus laevis	P84233
H3	Distal	e	canonical H3	Xenopus laevis	P84233
H4	Proximal	b	canonical H4	Xenopus laevis	P62799
H4	Distal	f	canonical H4	Xenopus laevis	P62799
H2A	Proximal	c	canonical H2A	Xenopus laevis	P06897
H2A	Distal	g	canonical H2A	Xenopus laevis	P06897
H2B	Proximal	d	canonical H2B	Xenopus laevis	P02281
H2B	Distal	h	canonical H2B	Xenopus laevis	P02281

Other proteins:

Chain	Name	UID
A	DNA-directed RNA polymerase subunit	A0A8D1DPV6
B	DNA-directed RNA polymerase subunit beta	I3LGP4
C	DNA-directed RNA polymerase II subunit RPB3	I3LCH3
D	RNA polymerase II subunit D	A0A287ADR4
E	DNA-directed RNA polymerase II subunit E	I3LSI7
F	DNA-directed RNA polymerase II subunit F	A0A4X1VEK9
G	DNA-directed RNA polymerase II subunit RPB7	I3LJZ9
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	I3LCB2
I	DNA-directed RNA polymerase II subunit RPB9	P60899
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	A0A4X1VYD0
K	DNA-directed RNA polymerase II subunit RPB11-a	F1RKE4
L	RNA polymerase II subunit K	A0A4X1TRS6
M	Transcription initiation factor IIB	Q00403
O	TATA-box-binding protein	P20226
Q	General transcription factor IIF subunit 1	P35269
R	General transcription factor IIF subunit 2	P13984
U	Transcription initiation factor IIA subunit 1	P52655
V	Transcription initiation factor IIA subunit 2	P52657

DNA:

Chain	Variant	Length
N	601	198
T	601	198

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.

H3p chain a

H4p chain b

H2Ap chain c

H2Bp chain d

H3d chain e

H4d chain f

H2Ad chain g

H2Bd chain h

DNA top chain N, bot chain T

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