6J50

RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation)

Exp. Method EM
Resolution, Å 4.7
Release Date 2019-02-20
Update Date 2024-03-27
Authors Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I.
Publication PMID: 30733384
doi 10.1126/science.aav8912
RCSB PDB 6J50
EMDB EMD-0675
Q-score 0.195
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
V Transcription elongation factor SPT4 C4R0E6
W Protein that forms a complex with Spt4p C4R370
DNA:
Chain Variant Length
0 601_modified 41
1 601_modified 41
N 601_modified 123
T 601_modified 128

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.