National Center for
Biotechnology Information

8CEO: Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome

PDB ID:

8CEO Download

MMDB ID:

227596

PDB Deposition Date:

2023/2/2

Updated in MMDB:

2024/07

Experimental Method:

electron microscopy

Resolution:

3.6 Å

Source Organism:

synthetic construct▼

Taxonomy	Molecule
synthetic construct	N, T
Xenopus laevis	r, s, t, v, w, x
Saccharomyces cerevisiae	0, 1, 2, 3, 4, 5, 6, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, O, Q, R, U, V, W, X, a, b, c, d, e, f , g, h, i, j, k, l, m, n, o, p, u, y

Similar Structures:

Biological Unit for 8CEO: 54-meric; determined by author

Molecular Components in 8CEO
Label	Count	Molecule
Proteins (52 molecules)
0	1	General Transcription and DNA Repair Factor IIH Helicase Subunit XPD
1	1	Tfb1 Isoform 1
2	1	RNA Polymerase II Transcription Factor B Subunit 2
3	1	RNA Polymerase II Transcription Factor B Subunit 3
4	1	General Transcription and DNA Repair Factor IIH Subunit Tfb4
5	1	General Transcription and DNA Repair Factor IIH Subunit Tfb5
6	1	General Transcription and DNA Repair Factor IIH
7	1	General Transcription and DNA Repair Factor IIH Helicase Subunit XPB
A	1	DNA-directed RNA Polymerase II Subunit Rpb1
B	1	DNA-directed RNA Polymerase II Subunit Rpb2
C	1	DNA-directed RNA Polymerase II Subunit Rpb3
D	1	DNA-directed RNA Polymerase II Subunit Rpb4
E	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc1
F	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc2
G	1	DNA-directed RNA Polymerase II Subunit Rpb7
H	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc3
I	1	DNA-directed RNA Polymerase II Subunit Rpb9
J	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc5
K	1	DNA-directed RNA Polymerase II Subunit Rpb11
L	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc4
M	1	Transcription Initiation Factor IIB
O	1	Tata-binding Protein
Q	1	Transcription Initiation Factor IIF Subunit Alpha
R	1	Transcription Initiation Factor IIF Subunit Beta
U	1	Toa1 Isoform 1
V	1	Transcription Initiation Factor IIA Subunit 2
W	1	Transcription Initiation Factor IIE Subunit Alpha
X	1	Transcription Initiation Factor IIE Subunit Beta
a	1	Mediator of RNA Polymerase II Transcription Subunit 6
b	1	Mediator of RNA Polymerase II Transcription Subunit 8
c	1	Mediator of RNA Polymerase II Transcription Subunit 11
d	1	Mediator of RNA Polymerase II Transcription Subunit 17
e	1	Mediator of RNA Polymerase II Transcription Subunit 18
f	1	Mediator of RNA Polymerase II Transcription Subunit 20
g	1	Mediator of RNA Polymerase II Transcription Subunit 22
h	1	Mediator of RNA Polymerase II Transcription Subunit 4
i	1	Mediator of RNA Polymerase II Transcription Subunit 7
j	1	Mediator of RNA Polymerase II Transcription Subunit 9
k	1	Mediator of RNA Polymerase II Transcription Subunit 10
l	1	Mediator of RNA Polymerase II Transcription Subunit 14
m	1	Mediator of RNA Polymerase II Transcription Subunit 19
n	1	Mediator of RNA Polymerase II Transcription Subunit 21
o	1	Mediator of RNA Polymerase II Transcription Subunit 31
p	1	Mediator of RNA Polymerase II Transcription Subunit 1
r v	2	Histone H3.2
s w	2	Histone H4
t x	2	Histone H2A
u y	2	Histone H2B
Nucleotides(2 molecules)
N	1	Nontemplate DNA (209-mer)
T	1	Template DNA (209-mer)
Chemicals and Non-standard biopolymers (19 molecules)
1	1	IRON/SULFUR CLUSTER
2	17	ZINC ION
3	1	MAGNESIUM ION

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303