SMTL ID : 8bvw.1

RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)

Coordinates
PDB Format
Method
ELECTRON MICROSCOPY
Oligo State
hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-mer
Ligands
1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Unassigned peptide, likely XPB(Non-covalent)
1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
17 x ZN: ZINC ION(Non-covalent)
1 x MG: MAGNESIUM ION(Non-covalent)
Links
RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP
Citation
Abril-Garrido, J. et al., Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Mol.Cell (2023)
Release Date
2023-05-03
Peptides
General transcription and DNA repair factor IIH helicase subunit XPB: A
TFIIH basal transcription factor complex helicase XPD subunit: B
General transcription factor IIH subunit 1: C
General transcription factor IIH subunit 4: D
General transcription factor IIH subunit 2: E
General transcription factor IIH subunit 3: F
General transcription factor IIH subunit 5: G
CDK-activating kinase assembly factor MAT1: H
Cyclin-dependent kinase 7: I
Cyclin-H: J
DNA-directed RNA polymerase subunit: K
DNA-directed RNA polymerase subunit beta: L
DNA-directed RNA polymerase II subunit RPB3: M
RNA polymerase II subunit D: N
DNA-directed RNA polymerase II subunit E: O
DNA-directed RNA polymerase II subunit F: P
DNA-directed RNA polymerase II subunit RPB7: Q
DNA-directed RNA polymerases I, II, and III subunit RPABC3: R
DNA-directed RNA polymerase II subunit RPB9: S
DNA-directed RNA polymerases I, II, and III subunit RPABC5: T
DNA-directed RNA polymerase II subunit RPB11-a: U
RNA polymerase II subunit K: V
Transcription initiation factor IIB: W
TATA-box-binding protein: Y
General transcription factor IIF subunit 1: Z
General transcription factor IIF subunit 2: 0
Transcription initiation factor IIA subunit 1: 2
Transcription initiation factor IIA subunit 2: 3
General transcription factor IIE subunit 1: 4
Transcription initiation factor IIE subunit beta: 5
Unassigned peptide, likely TFIIE-beta: 6
Histone H3.2: 7b
Histone H4: 8c
Histone H2A type 1: 9d
Histone H2B 1.1: ae
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
0
B
1
C
2
D
3
E
4
F
5
G
6
H
7
I
8
J
9
K
A
L
B
M
C
N
D
O
E
P
F
Q
G
R
H
S
I
T
J
U
K
V
L
W
M
Y
O
Z
Q
0
R
2
U
3
V
4
W
5
X
6
Z
7
a
b
e
8
b
c
f
9
c
d
g
a
d
e
h

General transcription and DNA repair factor IIH helicase subunit XPB

TFIIH basal transcription factor complex helicase XPD subunit

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4

General transcription factor IIH subunit 2

General transcription factor IIH subunit 3

General transcription factor IIH subunit 5

CDK-activating kinase assembly factor MAT1

Cyclin-dependent kinase 7

Cyclin-H

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RNA polymerase II subunit D

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerase II subunit F

DNA-directed RNA polymerase II subunit RPB7

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11-a

RNA polymerase II subunit K

Transcription initiation factor IIB

TATA-box-binding protein

General transcription factor IIF subunit 1

General transcription factor IIF subunit 2

Transcription initiation factor IIA subunit 1

Transcription initiation factor IIA subunit 2

General transcription factor IIE subunit 1

Transcription initiation factor IIE subunit beta

Unassigned peptide, likely TFIIE-beta

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

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