SMTL ID : 9j0p.1

Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc)

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: 5 residues within 4Å: Chain A: C.71, C.74, C.81, P.82, 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: 5 residues within 4Å: Chain A: C.111, C.114, K.116, C.184, Y.187 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.184 ZN.4: 4 residues within 4Å: Chain B: C.1119, 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: 4 residues within 4Å: Chain C: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.94, C:C.97 ZN.6: 4 residues within 4Å: Chain I: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 ZN.7: 4 residues within 4Å: Chain I: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.8: 4 residues within 4Å: Chain J: C.7, C.10, 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: 5 residues within 4Å: Chain L: C.19, C.22, C.36, E.38, C.39 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.19, L:C.22, L:C.36, L:C.39 ZN.10: 4 residues within 4Å: Chain M: C.17, C.20, C.34, C.37 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.17, M:C.20, M:C.34, M:C.37

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.495, D.497, D.499 Chain Q: G.12, U.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naganuma, M. et al., Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome. Sci Adv (2025)

Release Date

2025-02-05

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerase II subunit RPB4: 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
RPB12: L
Transcription elongation factor SPT4: M
Transcription elongation factor SPT5: N
Negative elongation factor A: R
Negative elongation factor B: S
Negative elongation factor C/D: T
Negative elongation factor E: U
Histone H3.3: VZ
Histone H4: W0
Histone H2A type 1-B/E: X1
Histone H2B type 1-J: Y2

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
Y

N
Z

R
U

S
V

T
W

U
X

V
a

Z
e

W
b

0
f

X
c

1
g

Y
d

2
h

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit RPB4

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

RPB12

Transcription elongation factor SPT4

Transcription elongation factor SPT5

Negative elongation factor A

Negative elongation factor B

Negative elongation factor C/D

Negative elongation factor E

Histone H3.3

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

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