SMTL ID : 8rbx.1

Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 9 residues within 4Å: Chain 0: N.1010, K.1013, E.1044, Q.1048 Chain 3: N.535, L.538, N.545, Y.547, D.548 3 PLIP interactions: 1 interactions with chain 0, 2 interactions with chain 3 Hydrogen bonds: 0:K.1013, 3:N.545, 3:D.548

10 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: C.111, C.114, C.154 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154 ZN.3: 4 residues within 4Å: Chain A: C.71, C.74, C.81, 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.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: 5 residues within 4Å: Chain I: C.17, E.19, 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: 4 residues within 4Å: Chain L: C.19, C.22, C.36, 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.12: 4 residues within 4Å: Chain 8: D.74, H.75, D.180, H.416 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:D.74, 8:H.75, 8:D.180, 8:H.416 ZN.13: 4 residues within 4Å: Chain 8: H.70, H.72, H.159, D.180 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:H.70, 8:H.72, 8:H.72, 8:H.159

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 2 residues within 4Å: Chain A: R.460 Chain P: G.17 No protein-ligand interaction detected (PLIP)

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.11: 4 residues within 4Å: Chain 3: D.631, E.632 Chain d: H.243, Y.267 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:D.631 MN.14: 5 residues within 4Å: Chain d: D.59, D.87, N.119, H.169, H.243 3 PLIP interactions: 3 interactions with chain d Metal complexes: d:D.87, d:H.169, d:H.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fianu, I. et al., Structural basis of Integrator-dependent RNA polymerase II termination. Nature (2024)

Release Date

2024-02-07

Peptides

DNA-directed RNA polymerase subunit: AX
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 polymerases I, II, and III subunit RPABC2: 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
Histone H3.3C: MS
Histone H4: OU
Histone H2A type 1: QV
Histone H2B type 1-J: RW
Transcription elongation factor SPT5: Y
Integrator complex subunit 1: Z
Integrator complex subunit 2: 0
Integrator complex subunit 4: 1
Integrator complex subunit 5: 2
Integrator complex subunit 6: 3
Integrator complex subunit 7: 4
Integrator complex subunit 8: 5
Integrator complex subunit 9: 6
Integrator complex subunit 10: 7
Integrator complex subunit 11: 8
Integrator complex subunit 13: 9
Integrator complex subunit 14: a
Integrator complex subunit 15: b
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform: c
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform: d
DSS1: e
Negative elongation factor A: f
NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B: g
Negative elongation factor C/D: h
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

X
Y

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

S
S

O
O

U
U

Q
Q

V
V

R
R

W
W

Y
Z

Z
a

0
b

1
d

2
e

3
f

4
g

5
h

6
i

7
j

8
k

9
m

a
n

b
o

c
p

d
q

e
r

f
u

g
v

h
w

i
x

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 polymerases I, II, and III subunit RPABC2

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

Histone H3.3C

Histone H4

Histone H2A type 1

Histone H2B type 1-J

Transcription elongation factor SPT5

Integrator complex subunit 1

Integrator complex subunit 2

Integrator complex subunit 4

Integrator complex subunit 5

Integrator complex subunit 6

Integrator complex subunit 7

Integrator complex subunit 8

Integrator complex subunit 9

Integrator complex subunit 10

Integrator complex subunit 11

Integrator complex subunit 13

Integrator complex subunit 14

Integrator complex subunit 15

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

DSS1

Negative elongation factor A

NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B

Negative elongation factor C/D

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK

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