SMTL ID : 7o75.1

Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA

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

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 10 residues within 4Å: Chain A: R.111, C.115, L.116, H.117, C.133, T.137, C.156, H.159, C.191, F.194 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.115, A:C.133, A:C.156, A:C.191

17 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain D: C.16, C.19, C.42, C.45 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.16, D:C.19, D:C.42, D:C.45 ZN.3: 4 residues within 4Å: Chain D: C.37, H.39, C.57, C.62 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.37, D:H.39, D:C.57, D:C.62 ZN.4: 4 residues within 4Å: Chain E: C.292, C.295, C.308, C.311 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.292, E:C.295, E:C.308, E:C.311 ZN.5: 5 residues within 4Å: Chain G: C.352, C.355, S.357, C.366, C.369 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.352, G:C.355, G:C.366, G:C.369 ZN.6: 5 residues within 4Å: Chain G: C.406, S.408, C.409, C.440, C.443 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.406, G:C.409, G:C.440, G:C.443 ZN.7: 4 residues within 4Å: Chain G: C.432, C.435, C.454, C.457 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.432, G:C.435, G:C.454, G:C.457 ZN.8: 4 residues within 4Å: Chain G: C.339, C.341, H.342, C.360 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.339, G:C.341, G:H.342, G:C.360 ZN.12: 4 residues within 4Å: Chain I: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.107, I:C.110, I:C.148, I:C.167 ZN.13: 4 residues within 4Å: Chain I: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.67, I:C.70, I:C.77, I:H.80 ZN.15: 4 residues within 4Å: Chain J: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.1163, J:C.1166, J:C.1182, J:C.1185 ZN.16: 4 residues within 4Å: Chain K: C.115, C.117, C.121, C.124 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.115, K:C.117, K:C.121, K:C.124 ZN.17: 5 residues within 4Å: Chain Q: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.7, Q:C.10, Q:C.29, Q:C.32 ZN.18: 4 residues within 4Å: Chain Q: C.75, C.78, C.103, C.106 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.75, Q:C.78, Q:C.103, Q:C.106 ZN.19: 4 residues within 4Å: Chain R: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.7, R:C.10, R:C.45, R:C.46 ZN.20: 4 residues within 4Å: Chain T: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.31, T:C.34, T:C.48, T:C.51 ZN.21: 4 residues within 4Å: Chain U: C.24, C.27, C.45, C.48 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.24, U:C.27, U:C.45, U:C.48 ZN.22: 4 residues within 4Å: Chain 2: C.124, C.127, C.149, C.152 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.124, 2:C.127, 2:C.149, 2:C.152

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.9: 8 residues within 4Å: Chain H: C.388, K.392, A.515, S.661, R.689, R.692 Ligands: MG.10, ADP.11 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain H: D.488, S.661, R.692 Ligands: BEF.9, ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain I: D.481, D.483, D.485 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.481, I:D.481, I:D.483, I:D.483, I:D.485

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 14 residues within 4Å: Chain H: Q.361, R.363, Q.366, G.389, A.390, G.391, K.392, T.393, L.394, W.427, D.663, R.692 Ligands: BEF.9, MG.10 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:Q.361, H:Q.366, H:G.389, H:A.390, H:G.391, H:K.392, H:T.393, H:T.393, H:T.393, H:D.663 Salt bridges: H:K.392, H:R.692, H:R.692 pi-Cation interactions: H:R.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schilbach, S. et al., Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening. Cell (2021)

Release Date

2021-06-16

Peptides

General transcription and DNA repair factor IIH helicase subunit XPD: A
General transcription and DNA repair factor IIH subunit TFB1: B
General transcription and DNA repair factor IIH subunit TFB2: C
RNA polymerase II transcription factor B subunit 3: D
General transcription and DNA repair factor IIH subunit TFB4: E
General transcription and DNA repair factor IIH subunit TFB5: F
General transcription and DNA repair factor IIH subunit SSL1: G
General transcription and DNA repair factor IIH helicase subunit XPB: H
DNA-directed RNA polymerase II subunit RPB1: I
DNA-directed RNA polymerase II subunit RPB2: J
DNA-directed RNA polymerase II subunit RPB3: K
DNA-directed RNA polymerase II subunit RPB4: L
DNA-directed RNA polymerases I, II, and III subunit RPABC1: M
DNA-directed RNA polymerases I, II, and III subunit RPABC2: N
DNA-directed RNA polymerase II subunit RPB7: O
DNA-directed RNA polymerases I, II, and III subunit RPABC3: P
DNA-directed RNA polymerase II subunit RPB9: Q
DNA-directed RNA polymerases I, II, and III subunit RPABC5: R
DNA-directed RNA polymerase II subunit RPB11: S
DNA-directed RNA polymerases I, II, and III subunit RPABC4: T
Transcription initiation factor IIB: U
TATA-box-binding protein: W
Transcription initiation factor IIF subunit alpha: X
Transcription initiation factor IIF subunit beta: Y
Transcription initiation factor IIA large subunit: 0
Transcription initiation factor IIA subunit 2: 1
Transcription initiation factor IIE subunit alpha: 2
Transcription initiation factor IIE subunit beta: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
2

D
3

E
4

F
5

G
6

H
7

I
A

J
B

K
C

L
D

M
E

N
F

O
G

P
H

Q
I

R
J

S
K

T
L

U
M

W
O

X
Q

Y
R

0
U

1
V

2
W

3
X

General transcription and DNA repair factor IIH helicase subunit XPD

General transcription and DNA repair factor IIH subunit TFB1

General transcription and DNA repair factor IIH subunit TFB2

RNA polymerase II transcription factor B subunit 3

General transcription and DNA repair factor IIH subunit TFB4

General transcription and DNA repair factor IIH subunit TFB5

General transcription and DNA repair factor IIH subunit SSL1

General transcription and DNA repair factor IIH helicase subunit XPB

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

Transcription initiation factor IIB

TATA-box-binding protein

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

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