SMTL ID : 4v1n.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 7.80 Å

Oligo State

hetero-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 R: 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: 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.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

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

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

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