9J0N

Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)

Exp. Method	EM
Resolution, Å	3.4
Release Date	2025-02-05
Update Date	2025-03-19
Authors	Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I.
doi	10.1126/sciadv.adu0577
Publication	PMID: 40043114
Related structures
RCSB PDB	9J0N
EMDB	EMD-61058
Q-score	0.316

Core histones in Nucleosome-like particles:

	Side	Chain	HistoneDB Variant	Taxa	UID
H3	Proximal	a	H3.3	Homo sapiens	P84243
H3	Distal	e	H3.3	Homo sapiens	P84243
H4	Proximal	b	canonical H4	Homo sapiens	P62805
H4	Distal	f	canonical H4	Homo sapiens	P62805
H2A	Proximal	c	canonical H2A	Homo sapiens	P04908
H2A	Distal	g	canonical H2A	Homo sapiens	P04908
H2B	Proximal	d	canonical H2B	Homo sapiens	P06899
H2B	Distal	h	canonical H2B	Homo sapiens	P06899

Other proteins:

Chain	Name	UID
A	DNA-directed RNA polymerase subunit	A0A8D1DPV6
B	DNA-directed RNA polymerase subunit beta	A0A0B8RVL1
C	DNA-directed RNA polymerase II subunit RPB3	I3LCH3
D	DNA-directed RNA polymerase II subunit RPB4	A0A481BYI6
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	A0A4X1VKG7
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	A0A8W4F9W9
K	DNA-directed RNA polymerase II subunit RPB11-a	F1RKE4
L	RPB12	A0A4X1TRS6
M	Transcription elongation factor A protein 1	P23193
U	Negative elongation factor A	Q9H3P2
V	Negative elongation factor B	Q8WX92
W	Negative elongation factor C/D	Q8IXH7
X	Negative elongation factor E	P18615
Y	Transcription elongation factor SPT4	P63272
Z	Transcription elongation factor SPT5	O00267

DNA:

Chain	Variant	Length
N	601_modified	156
T	601_modified	167

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 T, bot chain N

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