SMTL ID : 8bz1.1

RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-mer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: G.63, C.71, T.73, C.74, C.81, G.83, H.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.74, A:C.81, A:H.84 ZN.2: 6 residues within 4Å: Chain A: C.111, C.114, K.116, C.154, G.183, C.184 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154 ZN.4: 5 residues within 4Å: Chain B: C.1119, L.1121, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1119, B:C.1122, B:C.1137, B:C.1140 ZN.5: 5 residues within 4Å: Chain C: C.90, E.92, F.93, C.94, C.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.90, C:E.92, C:C.94, C:C.97 ZN.6: 7 residues within 4Å: Chain I: C.17, E.19, C.20, N.22, C.39, C.42, Y.44 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 ZN.7: 7 residues within 4Å: Chain I: C.86, C.89, H.91, C.114, A.116, C.119, H.121 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.8: 7 residues within 4Å: Chain J: C.7, T.9, C.10, K.12, R.42, C.44, C.45 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.44, J:C.45 ZN.9: 7 residues within 4Å: Chain L: C.19, E.21, C.22, C.36, E.38, C.39, Y.41 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.19, L:C.22, L:C.36 ZN.10: 2 residues within 4Å: Chain M: N.17, H.18 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:H.18

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: R.460, D.495, D.497, G.498, D.499 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.495, A:D.495, A:D.497, A:D.499, A:D.499

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

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
RNA polymerase II subunit D: D
DNA-directed RNA polymerase II subunit E: E
DNA-directed RNA polymerase II subunit F: F
DNA-directed RNA polymerase II subunit RPB7: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5: J
DNA-directed RNA polymerase II subunit RPB11-a: K
RNA polymerase II subunit K: L
Transcription initiation factor IIB: M
TATA-box-binding protein: O
General transcription factor IIF subunit 1: P
General transcription factor IIF subunit 2: Q
Transcription initiation factor IIA subunit 1: S
Transcription initiation factor IIA subunit 2: T
Histone H3.2: UY
Histone H4: VZ
Histone H2A type 1: W0
Histone H2B 1.1: X1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

O
O

P
Q

Q
R

S
U

T
V

U
a

Y
e

V
b

Z
f

W
c

0
g

X
d

1
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

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

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