SMTL ID : 5sva.1

Mediator-RNA Polymerase II Pre-Initiation Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.167 ZN.2: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 ZN.4: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.5: 5 residues within 4Å: Chain C: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.86, C:C.88, C:C.92, C:C.95 ZN.6: 4 residues within 4Å: Chain I: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.7, I:C.10, I:C.29, I:C.32 ZN.7: 4 residues within 4Å: Chain I: C.75, C.78, C.103, C.106 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103, I:C.106 ZN.8: 4 residues within 4Å: Chain J: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45, J:C.46 ZN.9: 4 residues within 4Å: Chain L: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.481, D.483, D.485 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.481, A:D.481, A:D.483, A:D.483, A:D.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, P.J. et al., Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell (2016)

Release Date

2016-09-28

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase II subunit RPB2: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerase II subunit RPB4: D
DNA-directed RNA polymerases I, II, and III subunit RPABC1: 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: K
DNA-directed RNA polymerases I, II, and III subunit RPABC4: L
Mediator of RNA polymerase II transcription subunit 6: M
Mediator of RNA polymerase II transcription subunit 8: N
Mediator of RNA polymerase II transcription subunit 11: O
Mediator of RNA polymerase II transcription subunit 17: P
Mediator of RNA polymerase II transcription subunit 18: Q
Mediator of RNA polymerase II transcription subunit 20: R
Mediator of RNA polymerase II transcription subunit 22: S
Mediator of RNA polymerase II transcription subunit 4: T
Mediator of RNA polymerase II transcription subunit 7: U
Mediator of RNA polymerase II transcription subunit 9: V
Mediator of RNA polymerase II transcription subunit 21: W
Mediator of RNA polymerase II transcription subunit 31: X
DNA repair helicase RAD3: Y
DNA repair helicase RAD25: Z
RNA polymerase II transcription factor B subunit 2: 0
RNA polymerase II transcription factor B subunit 5: 1
Transcription initiation factor IIB: 2
Transcription initiation factor IIA large subunit: 3
Transcription initiation factor IIA subunit 2: 4
Transcription initiation factor IIF subunit alpha: 5
Transcription initiation factor IIF subunit beta: 6
Transcription initiation factor IIE subunit alpha: 7
Transcription initiation factor IIE subunit beta: 8
TATA-box-binding protein: 9
DNA-directed RNA polymerase II subunit RPB1: a
Transcription initiation factor TFIID subunit 14: d

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

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

2
c

3
d

4
e

5
f

6
g

7
h

8
i

9
j

a
k

d
n

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit RPB4

DNA-directed RNA polymerases I, II, and III subunit RPABC1

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

DNA-directed RNA polymerases I, II, and III subunit RPABC4

Mediator of RNA polymerase II transcription subunit 6

Mediator of RNA polymerase II transcription subunit 8

Mediator of RNA polymerase II transcription subunit 11

Mediator of RNA polymerase II transcription subunit 17

Mediator of RNA polymerase II transcription subunit 18

Mediator of RNA polymerase II transcription subunit 20

Mediator of RNA polymerase II transcription subunit 22

Mediator of RNA polymerase II transcription subunit 4

Mediator of RNA polymerase II transcription subunit 7

Mediator of RNA polymerase II transcription subunit 9

Mediator of RNA polymerase II transcription subunit 21

Mediator of RNA polymerase II transcription subunit 31

DNA repair helicase RAD3

DNA repair helicase RAD25

RNA polymerase II transcription factor B subunit 2

RNA polymerase II transcription factor B subunit 5

Transcription initiation factor IIB

Transcription initiation factor IIA large subunit

Transcription initiation factor IIA subunit 2

Transcription initiation factor IIF subunit alpha

Transcription initiation factor IIF subunit beta

Transcription initiation factor IIE subunit alpha

Transcription initiation factor IIE subunit beta

TATA-box-binding protein

DNA-directed RNA polymerase II subunit RPB1

Transcription initiation factor TFIID subunit 14

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