8HE5

RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome

Exp. Method EM
Resolution, Å 6.95
Release Date 2023-07-05
Update Date 2023-07-05
Authors Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H.
Publication PMID: 37120012
doi 10.1016/j.jmb.2023.168130
Related structures 7WBV, 7WBW, 7WBX
RCSB PDB 8HE5
EMDB EMD-34685
Q-score 0.105
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal a canonical H3 Homo sapiens P68431
Distal e canonical H3 Homo sapiens P68431
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 C4QY79
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
M Transcription elongation factor 1 homolog C4QZ45
O DNA repair protein C4R198
DNA:
Chain Variant Length
N 601_modified 142
T 601_modified 154

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.