SMTL ID : 8s51.1

RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt

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-mer

Ligands

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

A-C-A-C-C-C-A-G.1: 32 residues within 4Å: Chain A: R.460, N.493, D.495, D.497, G.498, D.499, T.854 Chain B: G.591, Q.594, R.610, R.617, P.641, H.644, K.856, Q.857, K.1060, K.1068, H.1179, K.1184 Chain M: W.52, R.53, S.65 Chain R: C.83, T.84, G.85, G.86, G.87, T.88, G.89, T.90, G.91 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

10 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.71, C.74, C.81, H.84 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.71, A:C.74, A:C.81, A:H.84, A:H.84 ZN.3: 5 residues within 4Å: Chain A: C.111, C.114, C.154, G.183, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154, A:C.184 ZN.5: 4 residues within 4Å: Chain B: C.1245, C.1248, C.1263, C.1266 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1245, B:C.1248, B:C.1263, B:C.1266 ZN.6: 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.7: 4 residues within 4Å: Chain I: C.17, C.20, C.39, 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.8: 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.9: 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.10: 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.11: 5 residues within 4Å: Chain M: C.15, N.17, H.18, C.34, C.37 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:C.15, M:H.18, M:H.18, M:C.34, M:C.37 ZN.12: 5 residues within 4Å: Chain U: C.129, C.132, F.136, C.154, C.157 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:C.129, U:C.154, U:C.157

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.495, D.497, D.499 Ligands: A-C-A-C-C-C-A-G.1, A-C-A-C-C-C-A-G.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, Y. et al., Three-step mechanism of promoter escape by RNA polymerase II. Mol.Cell (2024)

Release Date

2024-04-17

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 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-a: K
RNA polymerase II subunit K: L
Transcription initiation factor IIB: M
TATA-box-binding protein: O
General transcription factor IIF subunit 1: P
General transcription factor IIF subunit 2: Q
Transcription initiation factor IIA subunit 1: S
Transcription initiation factor IIA subunit 2: T
General transcription factor IIE subunit 1: U
Transcription initiation factor IIE subunit beta: V

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

S
U

T
V

U
W

V
X

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 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-a

RNA polymerase II subunit K

Transcription initiation factor IIB

TATA-box-binding protein

General transcription factor IIF subunit 1

General transcription factor IIF subunit 2

Transcription initiation factor IIA subunit 1

Transcription initiation factor IIA subunit 2

General transcription factor IIE subunit 1

Transcription initiation factor IIE subunit beta

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