SMTL ID : 7nw0.1

RNA polymerase II pre-initiation complex with open promoter DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Unassigned peptide, likely XPB(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 7 residues within 4Å: Chain H: R.198, L.199, R.200, Q.266, T.267, V.268, S.269 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:T.267, H:V.268, H:V.268 Hydrogen bonds: H:R.198, H:R.198, H:T.267, H:T.267, H:S.269, H:S.269

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

SF4.2: 8 residues within 4Å: Chain A: C.116, H.118, C.134, C.155, F.157, Y.158, C.190, F.193 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.116, A:C.134, A:C.155, A:C.190

15 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain E: C.268, C.271, C.282, C.285 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.268, E:C.271, E:C.282, E:C.285 ZN.4: 4 residues within 4Å: Chain E: C.255, C.257, H.258, C.276 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.255, E:C.257, E:H.258, E:H.258, E:C.276 ZN.5: 4 residues within 4Å: Chain G: C.345, C.348, C.368, C.371 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.345, G:C.348, G:C.368, G:C.371 ZN.6: 4 residues within 4Å: Chain G: C.360, C.363, C.382, C.385 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.360, G:C.363, G:C.382, G:C.385 ZN.7: 4 residues within 4Å: Chain G: C.291, C.294, C.305, C.308 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.291, G:C.294, G:C.305, G:C.308 ZN.11: 4 residues within 4Å: Chain I: C.71, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.71, I:C.74, I:C.81, I:H.84 ZN.12: 5 residues within 4Å: Chain I: C.111, C.114, C.154, G.183, C.184 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:C.111, I:C.114, I:C.154, I:G.183, I:C.184 ZN.14: 4 residues within 4Å: Chain J: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.1119, J:C.1122, J:C.1137, J:C.1140 ZN.15: 4 residues within 4Å: Chain K: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.88, K:C.90, K:C.94, K:C.97 ZN.16: 4 residues within 4Å: Chain Q: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.17, Q:C.20, Q:C.39, Q:C.42 ZN.17: 4 residues within 4Å: Chain Q: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.86, Q:C.89, Q:C.114, Q:C.119 ZN.18: 4 residues within 4Å: Chain R: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.7, R:C.10, R:C.44, R:C.45 ZN.19: 4 residues within 4Å: Chain T: C.19, C.22, C.36, C.39 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.19, T:C.22, T:C.36, T:C.39 ZN.20: 4 residues within 4Å: Chain U: C.15, H.18, C.34, C.37 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:C.15, U:H.18, U:H.18, U:C.34, U:C.37 ZN.21: 4 residues within 4Å: Chain 2: C.129, F.136, C.154, C.157 3 PLIP interactions: 3 interactions with chain 2 Metal complexes: 2:C.129, 2:C.154, 2:C.157

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

ADP.8: 16 residues within 4Å: Chain H: V.315, R.317, Q.320, G.343, A.344, G.345, K.346, S.347, L.348, Q.377, W.381, D.616, P.618, R.645 Ligands: MG.9, BEF.10 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:R.317, H:Q.320, H:Q.320, H:G.343, H:A.344, H:G.345, H:K.346, H:S.347, H:S.347, H:S.347, H:Q.377, H:D.616 Salt bridges: H:K.346, H:R.645, H:R.645 pi-Cation interactions: H:R.317, H:R.317

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain H: S.347, D.441 Ligands: ADP.8, BEF.10 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain I: D.495, D.497, D.499 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.495, I:D.495, I:D.497, I:D.497, I:D.499

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

BEF.10: 8 residues within 4Å: Chain H: C.342, K.346, A.468, S.614, R.642, R.645 Ligands: ADP.8, MG.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aibara, S. et al., Structures of mammalian RNA polymerase II pre-initiation complexes. Nature (2021)

Release Date

2021-05-05

Peptides

TFIIH basal transcription factor complex helicase XPD subunit: A
General transcription factor IIH subunit 1: B
General transcription factor IIH subunit 4: C
CDK-activating kinase assembly factor MAT1: D
General transcription factor IIH subunit 3: E
General transcription factor IIH subunit 5: F
General transcription factor IIH subunit 2: G
General transcription and DNA repair factor IIH helicase subunit XPB: H
RPB1: I
DNA-directed RNA polymerase subunit beta: J
DNA-directed RNA polymerase II subunit RPB3: K
RPOL4c domain-containing protein: L
DNA-directed RNA polymerase II subunit E: M
DNA-directed RNA polymerase II subunit F: 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
RNA_pol_L_2 domain-containing protein: S
RNA polymerase II subunit K: T
Transcription initiation factor IIB: U
TATA-box-binding protein: W
General transcription factor IIF subunit 1: X
General transcription factor IIF subunit 2: Y
Transcription initiation factor IIA subunit 1: 0
Transcription initiation factor IIA subunit 2: 1
General transcription factor IIE subunit 1: 2
Transcription initiation factor IIE subunit beta: 3
Unassigned peptide, likely TFIIE-Beta: 4

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

4
Y

TFIIH basal transcription factor complex helicase XPD subunit

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4

CDK-activating kinase assembly factor MAT1

General transcription factor IIH subunit 3

General transcription factor IIH subunit 5

General transcription factor IIH subunit 2

General transcription and DNA repair factor IIH helicase subunit XPB

RPB1

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RPOL4c domain-containing protein

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerase II subunit F

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

RNA_pol_L_2 domain-containing protein

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

Unassigned peptide, likely TFIIE-Beta

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