SMTL ID : 9j0n.1

Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.71, T.73, 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, G.182, 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: 5 residues within 4Å: Chain A: M.34 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 H: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.17, H:C.20, H:C.39, H:C.42 ZN.7: 4 residues within 4Å: Chain H: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.86, H:C.89, H:C.114, H:C.119 ZN.8: 4 residues within 4Å: Chain I: C.17, C.20, C.34, C.37 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.34, I:C.37 ZN.9: 4 residues within 4Å: Chain O: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.7, O:C.10, O:C.44, O:C.45 ZN.10: 5 residues within 4Å: Chain Q: C.19, C.22, C.36, E.38, C.39 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.19, Q:C.22, Q:C.36, Q:C.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.495, D.497, D.499 Chain L: C.41, C.42 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.497, A:D.497, A:D.499

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 E: D
DNA-directed RNA polymerase II subunit F: E
DNA-directed RNA polymerase II subunit RPB7: F
DNA-directed RNA polymerases I, II, and III subunit RPABC3: G
DNA-directed RNA polymerase II subunit RPB9: H
Transcription elongation factor SPT4: I
Transcription elongation factor SPT5: J
DNA-directed RNA polymerase II subunit RPB4: N
DNA-directed RNA polymerases I, II, and III subunit RPABC5: O
DNA-directed RNA polymerase II subunit RPB11-a: P
RPB12: Q
Transcription elongation factor A protein 1: R
Histone H3.3: SW
Histone H4: TX
Histone H2A type 1-B/E: UY
Histone H2B type 1-J: VZ
Negative elongation factor A: 0
Negative elongation factor B: 1
Negative elongation factor C/D: 2
Negative elongation factor E: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

G
H

H
I

I
Y

J
Z

N
D

O
J

P
K

Q
L

R
M

S
a

W
e

T
b

X
f

U
c

Y
g

V
d

Z
h

0
U

1
V

2
W

3
X

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

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

Transcription elongation factor SPT4

Transcription elongation factor SPT5

DNA-directed RNA polymerase II subunit RPB4

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

DNA-directed RNA polymerase II subunit RPB11-a

RPB12

Transcription elongation factor A protein 1

Histone H3.3

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

Negative elongation factor A

Negative elongation factor B

Negative elongation factor C/D

Negative elongation factor E

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