SMTL ID : 4v1o.1

Architecture of the RNA polymerase II-Mediator core transcription initiation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 9.70 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-mer

Ligands

1 x A- U- A- U- C- A: RNA(Non-covalent)

A-U-A-U-C-A.1: 20 residues within 4Å: Chain A: R.446, D.483, D.485 Chain B: A.477, Q.481, Q.776, K.979, K.987, H.1097, K.1102 Chain M: D.70, N.72, D.74 Chain S: T.15, G.16, A.17, T.18, A.19, T.20 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

9 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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.5: 5 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 Chain D: K.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.6: 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.7: 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.8: 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.9: 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.10: 5 residues within 4Å: Chain L: C.31, C.34, S.36, 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 ZN.11: 4 residues within 4Å: Chain M: C.24, C.27, C.45, C.48 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.24, M:C.27, M:C.45, M:C.48

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.481, D.483, D.485 Ligands: A-U-A-U-C-A.1 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

Plaschka, C. et al., Architecture of the RNA Polymerase II-Mediator Core Initiation Complex. Nature (2015)

Release Date

2015-02-04

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 RPABC 1: E
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2: F
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7: G
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3: H
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9: I
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5: J
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11: K
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4: L
TRANSCRIPTION INITIATION FACTOR IIB: M
TATA-BOX-BINDING PROTEIN: O
TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ALPHA: P
TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA: Q
MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 6: R
MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 8: T
MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 20: U
MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 11: V
MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 18: W
MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 20: X
MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 22: Y

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

O
O

P
Q

Q
R

R
S

T
U

U
V

V
W

W
X

X
Y

Y
Z

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 RPABC 1

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4

TRANSCRIPTION INITIATION FACTOR IIB

TATA-BOX-BINDING PROTEIN

TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ALPHA

TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA

MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 6

MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 8

MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 20

MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 11

MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 18

MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 20

MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 22

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