8CEO

Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome

Exp. Method EM
Resolution, Å 3.6
Release Date 2023-03-08
Update Date 2023-04-19
Authors Schilbach, S., Wang, H., Dienemann, C., Cramer, P.
Publication PMID: 37014863
doi 10.1073/pnas.2220542120
RCSB PDB 8CEO
EMDB EMD-16611
Q-score 0.222
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal r canonical H3 Xenopus laevis P84233
Distal v canonical H3 Xenopus laevis P84233
H4 Proximal s canonical H4 Xenopus laevis P62799
Distal w canonical H4 Xenopus laevis P62799
H2A Proximal t canonical H2A Xenopus laevis P06897
Distal x canonical H2A Xenopus laevis P06897
H2B Proximal u canonical H2B Saccharomyces cerevisiae P02281
Distal y canonical H2B Saccharomyces cerevisiae P02281
Other proteins:
Chain Name UID
0 General transcription and DNA repair factor IIH helicase subunit XPD P06839
1 TFB1 isoform 1 P32776
2 RNA polymerase II transcription factor B subunit 2 Q02939
3 RNA polymerase II transcription factor B subunit 3 Q03290
4 General transcription and DNA repair factor IIH subunit TFB4 Q12004
5 General transcription and DNA repair factor IIH subunit TFB5 Q3E7C1
6 General transcription and DNA repair factor IIH Q04673
7 General transcription and DNA repair factor IIH helicase subunit XPB Q00578
A DNA-directed RNA polymerase II subunit RPB1 P04050
B DNA-directed RNA polymerase II subunit RPB2 P08518
C DNA-directed RNA polymerase II subunit RPB3 P16370
D DNA-directed RNA polymerase II subunit RPB4 P20433
E DNA-directed RNA polymerases I, II, and III subunit RPABC1 P20434
F DNA-directed RNA polymerases I, II, and III subunit RPABC2 P20435
G DNA-directed RNA polymerase II subunit RPB7 P34087
H DNA-directed RNA polymerases I, II, and III subunit RPABC3 P20436
I DNA-directed RNA polymerase II subunit RPB9 P27999
J DNA-directed RNA polymerases I, II, and III subunit RPABC5 P22139
K DNA-directed RNA polymerase II subunit RPB11 P38902
L DNA-directed RNA polymerases I, II, and III subunit RPABC4 P40422
M Transcription initiation factor IIB P29055
O TATA-binding protein P13393
Q Transcription initiation factor IIF subunit alpha P41895
R Transcription initiation factor IIF subunit beta P41896
U TOA1 isoform 1 P32773
V Transcription initiation factor IIA subunit 2 P32774
W Transcription initiation factor IIE subunit alpha P36100
X Transcription initiation factor IIE subunit beta P36145
a Mediator of RNA polymerase II transcription subunit 6 P38782
b Mediator of RNA polymerase II transcription subunit 8 P38304
c Mediator of RNA polymerase II transcription subunit 11 Q99278
d Mediator of RNA polymerase II transcription subunit 17 P32569
e Mediator of RNA polymerase II transcription subunit 18 P32585
f Mediator of RNA polymerase II transcription subunit 20 P34162
g Mediator of RNA polymerase II transcription subunit 22 P32570
h Mediator of RNA polymerase II transcription subunit 4 Q12343
i Mediator of RNA polymerase II transcription subunit 7 Q08278
j Mediator of RNA polymerase II transcription subunit 9 P33308
k Mediator of RNA polymerase II transcription subunit 10 Q06213
l Mediator of RNA polymerase II transcription subunit 14 P19263
m Mediator of RNA polymerase II transcription subunit 19 P25046
n Mediator of RNA polymerase II transcription subunit 21 P47822
o Mediator of RNA polymerase II transcription subunit 31 P38633
p Mediator of RNA polymerase II transcription subunit 1 Q12321
DNA:
Chain Variant Length
N 601 209
T 601 209

H3

H4

H2A

H2B

DNA

Other


Chain Bfactor Q-score Local Resolution

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.