8JH3

RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome

Exp. Method EM
Resolution, Å 3.7
Release Date 2023-11-29
Update Date 2023-12-20
Authors Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H.
Publication PMID: 37981206
doi 10.1016/j.jbc.2023.105477
RCSB PDB 8JH3
EMDB EMD-36252
Q-score 0.255
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal a H3.3 Homo sapiens P84243
Distal e H3.3 Homo sapiens P84243
H4 Proximal b canonical H4 Homo sapiens P62805
Distal f canonical H4 Homo sapiens P62805
H2A Proximal c canonical H2A Homo sapiens P04908
Distal g canonical H2A Homo sapiens P04908
H2B Proximal d canonical H2B Homo sapiens P06899
Distal h canonical H2B Homo sapiens P06899
Other proteins:
Chain Name UID
A DNA-directed RNA polymerase subunit C4R4Y0
B DNA-directed RNA polymerase subunit beta C4QZQ7
C RNA polymerase II third largest subunit B44, part of central core C4R7L2
D RNA polymerase II subunit B32 C4R2U9
E DNA-directed RNA polymerases I, II, and III subunit RPABC1 C4R3P8
F RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III C4R1V1
G RNA polymerase II subunit C4R9A1
H DNA-directed RNA polymerases I, II, and III subunit RPABC3 C4R273
I DNA-directed RNA polymerase subunit F2QPE6
J RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III C4R009
K RNA polymerase II subunit B12.5 C4R3Z5
L RNA polymerase subunit ABC10-alpha F2QMI1
DNA:
Chain Variant Length
N 601_modified 141
T 601_modified 159

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.