6A5T

RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome

Exp. Method EM
Resolution, Å 6.7
Release Date 2018-10-03
Update Date 2024-03-27
Authors Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H.
Publication PMID: 30287617
doi 10.1126/science.aau9904
RCSB PDB 6A5T
EMDB EMD-6984
Q-score 0.151
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 RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III 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 117
T 601_modified 126

H3

H4

H2A

H2B

DNA

Other


Chain Bfactor Q-score

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.