SMTL ID : 7ml2.1

RNA polymerase II pre-initiation complex (PIC3)

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-mer

Ligands

17 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.107, C.110, C.148, G.166, 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: 5 residues within 4Å: Chain A: G.59, 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: 6 residues within 4Å: Chain I: C.7, C.10, N.12, C.29, T.31, 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: 7 residues within 4Å: Chain I: C.75, C.78, S.80, C.103, S.105, C.106, H.108 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:C.75, I:C.78, I:S.80, I:S.105, I:C.106 ZN.8: 5 residues within 4Å: Chain J: C.7, C.10, R.43, 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: 6 residues within 4Å: Chain L: C.31, C.34, S.36, C.48, K.49, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.48, L:K.49, L:C.51 ZN.10: 5 residues within 4Å: Chain M: C.24, E.26, 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 ZN.11: 4 residues within 4Å: Chain R: C.124, C.127, C.149, C.152 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.124, R:C.127, R:C.149, R:C.152 ZN.12: 4 residues within 4Å: Chain X: C.289, C.292, C.305, C.308 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.289, X:C.292, X:C.305, X:C.308 ZN.14: 4 residues within 4Å: Chain Z: C.403, C.406, C.437, C.440 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.403, Z:C.406, Z:C.437, Z:C.440 ZN.15: 4 residues within 4Å: Chain Z: C.429, C.432, C.451, C.454 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.429, Z:C.432, Z:C.451, Z:C.454 ZN.16: 6 residues within 4Å: Chain Z: C.349, N.351, C.352, H.353, C.363, C.366 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.349, Z:C.352, Z:C.363, Z:C.366 ZN.17: 4 residues within 4Å: Chain Z: C.336, C.338, H.339, C.357 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.336, Z:C.338, Z:H.339, Z:C.357 ZN.18: 5 residues within 4Å: Chain 3: C.13, I.15, C.16, C.39, S.41 2 PLIP interactions: 2 interactions with chain 3 Metal complexes: 3:C.13, 3:C.39 ZN.19: 5 residues within 4Å: Chain 3: C.34, Y.35, H.36, C.54, L.63 3 PLIP interactions: 3 interactions with chain 3 Metal complexes: 3:C.34, 3:C.34, 3:H.36

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.483, A:D.483, A:D.485, A:D.485

1 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.13: 12 residues within 4Å: Chain Y: C.115, L.116, H.117, V.120, C.133, T.137, C.156, Y.158, H.159, C.191, Y.193, F.194 4 PLIP interactions: 4 interactions with chain Y, Metal complexes: Y:C.115, Y:C.115, Y:C.133, Y:C.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, C. et al., Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Mol.Cell (2022)

Release Date

2022-02-02

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: 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 II subunit RPABC5: J
DNA-directed RNA polymerase II subunit RPB11: K
DNA-directed RNA polymerases II subunit RPABC4: L
Transcription initiation factor IIB: M
Transcription initiation factor IIF subunit alpha: N
Transcription initiation factor IIF subunit beta: O
Transcription initiation factor IIA large subunit: P
Transcription initiation factor IIA subunit 2: Q
Transcription initiation factor IIE subunit alpha: R
Transcription initiation factor IIE subunit beta: S
BJ4_G0004860.mRNA.1.CDS.1: V
Tfb1: W
Tfb4: X
General transcription and DNA repair factor IIH helicase subunit XPD: Y
General transcription and DNA repair factor IIH: Z
RNA polymerase II transcription factor B subunit 2: 0
General transcription and DNA repair factor IIH subunit TFB5: 1
General transcription and DNA repair factor IIH helicase subunit XPB: 2
BJ4_G0050160.mRNA.1.CDS.1: 3

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
Q

O
R

P
U

Q
V

R
W

S
X

V
O

W
1

X
4

Y
0

Z
6

0
2

1
5

2
7

3
3

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

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 II subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11

DNA-directed RNA polymerases II subunit RPABC4

Transcription initiation factor IIB

Transcription initiation factor IIF subunit alpha

Transcription initiation factor IIF subunit beta

Transcription initiation factor IIA large subunit

Transcription initiation factor IIA subunit 2

Transcription initiation factor IIE subunit alpha

Transcription initiation factor IIE subunit beta

BJ4_G0004860.mRNA.1.CDS.1

Tfb1

Tfb4

General transcription and DNA repair factor IIH helicase subunit XPD

General transcription and DNA repair factor IIH

RNA polymerase II transcription factor B subunit 2

General transcription and DNA repair factor IIH subunit TFB5

General transcription and DNA repair factor IIH helicase subunit XPB

BJ4_G0050160.mRNA.1.CDS.1

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