7XTI

RNA polymerase II elongation complex transcribing a nucleosome (EC58hex)

Exp. Method EM
Resolution, Å 3.9
Release Date 2022-10-12
Update Date 2022-10-12
Authors Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I.
Publication PMID: 35981082
doi 10.1126/science.abp9466
RCSB PDB 7XTI
EMDB EMD-33450
Q-score 0.223
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal e H3.3 Homo sapiens P84243
Distal a H3.3 Homo sapiens P84243
H4 Proximal f canonical H4 Homo sapiens P62805
Distal b canonical H4 Homo sapiens P62805
H2A Proximal g canonical H2A Homo sapiens P04908
H2B Proximal 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
M Transcription elongation factor 1 homolog C4QZ45
V Transcription elongation factor SPT4 C4R0E6
W Transcription elongation factor SPT5 C4R370
j FACT complex subunit C4QYQ8
k FACT complex subunit POB3 F2QNN8
m Transcription elongation factor Spt6 C4R7H2
n Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II C4R7L8
q Component of the Paf1p complex C4R6B2
r RNAPII-associated chromatin remodeling Paf1 complex subunit F2QQ42
u Leo1 C4R3K1
v RNAP II-associated protein C4R997
x Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p C4R1E6
DNA:
Chain Variant Length
N 601_modified 74
T 601_modified 85

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.