7NKX

RNA polymerase II-Spt4/5-nucleosome-Chd1 structure

Exp. Method EM
Resolution, Å 2.9
Release Date 2021-08-25
Update Date 2021-08-25
Authors Farnung, L., Ochmann, M., Engeholm, M., Cramer, P.
Publication PMID: 33846633
doi 10.1038/s41594-021-00578-6
RCSB PDB 7NKX
EMDB EMD-12449
Q-score 0.444
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal a canonical H3 Xenopus laevis P84233
Distal e canonical H3 Xenopus laevis P84233
H4 Proximal b canonical H4 Xenopus laevis P62799
Distal f canonical H4 Xenopus laevis P62799
H2A Proximal c canonical H2A Xenopus laevis P06897
Distal g canonical H2A Xenopus laevis P06897
H2B Proximal d canonical H2B Xenopus laevis P02281
Distal h canonical H2B Xenopus laevis P02281
Other proteins:
Chain Name UID
A DNA-directed RNA polymerase II subunit RPB1 P04050
B DNA-directed RNA polymerase II subunit RPB2 P08518
C DNA-directed RNA polymerase II subunit RPB3 P16370
D DNA-directed RNA polymerase II subunit RPB4 P20433
E DNA-directed RNA polymerases I, II, and III subunit RPABC1 P20434
F DNA-directed RNA polymerases I, II, and III subunit RPABC2 P20435
G DNA-directed RNA polymerase II subunit RPB7 P34087
H DNA-directed RNA polymerases I, II, and III subunit RPABC3 P20436
I DNA-directed RNA polymerase II subunit RPB9 P27999
J DNA-directed RNA polymerases I, II, and III subunit RPABC5 P22139
K DNA-directed RNA polymerase II subunit RPB11 P38902
L DNA-directed RNA polymerases I, II, and III subunit RPABC4 P40422
W Chromo domain-containing protein 1 P32657
Y Chromatin elongation factor SPT4 P32914
Z Transcription elongation factor SPT5 P27692
DNA:
Chain Variant Length
N 601 128
T 601_modified 139

H3

H4

H2A

H2B

DNA

Other


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.