SMTL ID : 7ycx.1

The structure of INTAC-PEC complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.18 Å

Oligo State

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

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain I: D.72, H.73, D.178, H.414 Chain Y: A.1 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.72, I:H.73, I:D.178, I:H.414 ZN.2: 7 residues within 4Å: Chain I: H.68, H.70, H.73, H.157, D.178 Chain Y: A.1 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.68, I:H.70, I:H.157, I:D.178 ZN.6: 4 residues within 4Å: Chain N: C.111, C.114, C.154, C.184 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.111, N:C.114, N:C.154, N:C.184 ZN.7: 4 residues within 4Å: Chain N: C.71, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.71, N:C.74, N:C.81, N:H.84 ZN.8: 4 residues within 4Å: Chain O: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.1119, O:C.1122, O:C.1137, O:C.1140 ZN.9: 4 residues within 4Å: Chain P: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.88, P:C.90, P:C.94, P:C.97 ZN.10: 5 residues within 4Å: Chain T: C.17, E.19, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.17, T:C.20, T:C.39, T:C.42 ZN.11: 5 residues within 4Å: Chain T: C.86, C.89, C.114, A.116, C.119 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.86, T:C.89, T:C.114, T:C.119 ZN.12: 6 residues within 4Å: Chain U: C.7, T.9, C.10, R.42, C.44, C.45 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.7, U:C.10, U:C.44, U:C.45 ZN.13: 5 residues within 4Å: Chain W: C.19, C.22, T.24, C.36, C.39 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.19, W:C.22, W:C.36, W:C.39

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

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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain N: D.495, D.497, D.499 Chain Y: U.23 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:D.495, N:D.497, N:D.499, N:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, H. et al., Structural basis of INTAC-regulated transcription. Protein Cell (2023)

Release Date

2023-03-15

Peptides

Integrator complex subunit 1: A
Integrator complex subunit 2: B
Integrator complex subunit 4: C
Integrator complex subunit 5: D
Integrator complex subunit 6: E
Integrator complex subunit 7: F
Integrator complex subunit 8: G
Integrator complex subunit 9: H
Integrator complex subunit 11: I
Unknown2: J
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform: K
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform: L
Unknown: M
DNA-directed RNA polymerase II subunit RPB1,DNA-directed RNA polymerase II subunit RPB1, CTD1, CTD2, CTD3, CTD4: N
DNA-directed RNA polymerase subunit beta: O
DNA-directed RNA polymerase II subunit RPB3: P
DNA-directed RNA polymerase II subunit E: Q
DNA-directed RNA polymerase II subunit F: R
DNA-directed RNA polymerases I, II, and III subunit RPABC3: S
DNA-directed RNA polymerase II subunit RPB9: T
DNA-directed RNA polymerases I, II, and III subunit RPABC5: U
RNA_pol_L_2 domain-containing protein: V
RPB12: W
Negative elongation factor A: 0
Negative elongation factor B: 1
Negative elongation factor C/D: 2
Negative elongation factor E: 3
Transcription elongation factor SPT4: 4
Transcription elongation factor SPT5: 5
DNA-directed RNA polymerase II subunit RPB7: 6
DNA-directed RNA polymerase II subunit RPB4: 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

G
H

H
I

I
K

J
M

K
P

L
Q

M
U

N
1

O
2

P
3

Q
4

R
5

S
6

T
7

U
8

V
9

W
a

0
e

1
f

2
g

3
h

4
i

5
j

6
k

7
l

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

Unknown2

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

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

Unknown

DNA-directed RNA polymerase II subunit RPB1,DNA-directed RNA polymerase II subunit RPB1, CTD1, CTD2, CTD3, CTD4

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 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

RPB12

Negative elongation factor A

Negative elongation factor B

Negative elongation factor C/D

Negative elongation factor E

Transcription elongation factor SPT4

Transcription elongation factor SPT5

DNA-directed RNA polymerase II subunit RPB7

DNA-directed RNA polymerase II subunit RPB4

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