SMTL ID : 7pks.1

Structural basis of Integrator-mediated transcription regulation

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-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain O: U.17 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.495, A:D.495, A:D.497, A:D.499

10 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.111, C.114, C.154, C.184, Q.188 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154, A:C.184 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, C.20, C.39, N.41, 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.10: 6 residues within 4Å: Chain 3: H.68, D.72, H.73, E.203, H.414 Ligands: ZN.11 3 PLIP interactions: 3 interactions with chain 3 Metal complexes: 3:D.72, 3:H.73, 3:H.414 ZN.11: 5 residues within 4Å: Chain 3: H.68, H.70, H.157, D.178 Ligands: ZN.10 3 PLIP interactions: 3 interactions with chain 3 Metal complexes: 3:H.68, 3:H.70, 3:H.157

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

MN.12: 6 residues within 4Å: Chain 5: D.57, D.85, N.117, H.167, H.241 Ligands: MN.13 3 PLIP interactions: 3 interactions with chain 5 Metal complexes: 5:D.85, 5:H.167, 5:H.241 MN.13: 5 residues within 4Å: Chain 5: D.57, H.59, D.85, H.241 Ligands: MN.12 3 PLIP interactions: 3 interactions with chain 5 Metal complexes: 5:D.57, 5:H.59, 5:D.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fianu, I. et al., Structural basis of Integrator-mediated transcription regulation. Science (2021)

Release Date

2021-12-08

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
RNA_pol_L_2 domain-containing protein: K
RNA polymerase II subunit K: L
RPBI C-terminal domain peptide: M
Negative elongation factor A: Q
Negative elongation factor B: R
Negative elongation factor C/D: S
Negative elongation factor E: T
Transcription elongation factor SPT5: U
Integrator complex subunit 1: V
Integrator complex subunit 2: W
Integrator complex subunit 4: X
Integrator complex subunit 5: Y
Integrator complex subunit 6: Z
Integrator complex subunit 7: 0
Integrator complex subunit 8: 1
Integrator complex subunit 9: 2
Integrator complex subunit 11: 3
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform: 4
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform: 5
Unknown: 6

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

Q
U

R
V

S
W

T
X

U
Z

V
a

W
b

X
d

Y
e

Z
f

0
g

1
h

2
i

3
k

4
p

5
q

6
u

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

RNA_pol_L_2 domain-containing protein

RNA polymerase II subunit K

RPBI C-terminal domain peptide

Negative elongation factor A

Negative elongation factor B

Negative elongation factor C/D

Negative elongation factor E

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 11

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

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

Unknown

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