SMTL ID : 8waq.1

Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-2-2-2-1-1-2-2-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x ILX- TRX- GLY- ILE- GLY- CSX- ASN- HYP: Alpha-amanitin(Non-covalent)

ILX-TRX-GLY-ILE-GLY-CSX-ASN-HYP.1: 23 residues within 4Å: Chain 5: N.742, N.746, R.749, D.750, G.753, I.779, S.782, Q.783, V.787, V.788, G.789, Q.790, Q.791, N.792, G.795, R.797, H.839, G.842, G.843, E.845, H.1108, Y.1109 Chain 6: Q.718 16 PLIP interactions: 15 interactions with chain 5, 1 interactions with chain 6 Hydrophobic interactions: 5:R.749, 5:I.779, 5:Q.783, 5:N.792 Hydrogen bonds: 5:N.746, 5:R.749, 5:S.782, 5:Q.783, 5:Q.790, 5:Q.791, 5:N.792, 5:N.792, 5:E.845, 6:Q.718 pi-Cation interactions: 5:R.749, 5:R.749

1 x ATP- U- C- A- A- C- G2L: RNA(Non-covalent)

ATP-U-C-A-A-C-G2L.2: 20 residues within 4Å: Chain 1: C.53, G.54, T.55, T.56, G.57, A.58, T.59, G.60 Chain 5: R.460, D.499 Chain 6: Q.468, E.516, Q.731, K.934, K.942, K.1052, H.1053, K.1058 Ligands: MG.15, W0F.16 3 PLIP interactions: 2 interactions with chain 6, 1 interactions with chain 5 Salt bridges: 6:K.934, 6:K.942 Hydrogen bonds: 5:R.460

17 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.6, C.9, T.12, K.13, C.31 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.9, A:C.9, A:C.31 ZN.4: 4 residues within 4Å: Chain A: C.26, H.28, C.46, C.49 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.26, A:H.28, A:C.46, A:C.49 ZN.5: 4 residues within 4Å: Chain C: C.345, C.348, C.368, C.371 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.345, C:C.348, C:C.368, C:C.371 ZN.6: 4 residues within 4Å: Chain C: C.360, C.363, C.382, C.385 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.360, C:C.363, C:C.382, C:C.385 ZN.7: 4 residues within 4Å: Chain C: C.291, C.294, C.305, C.308 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.291, C:C.294, C:C.305, C:C.308 ZN.8: 4 residues within 4Å: Chain D: C.268, C.271, C.282, C.285 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.268, D:C.271, D:C.282, D:C.285 ZN.9: 4 residues within 4Å: Chain D: C.255, C.257, H.258, C.276 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.255, D:C.257, D:H.258, D:C.276 ZN.11: 4 residues within 4Å: Chain V: C.15, H.18, C.34, C.37 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:C.15, V:H.18, V:H.18, V:C.34, V:C.37 ZN.12: 5 residues within 4Å: Chain Y: C.129, V.131, C.132, C.154, C.157 2 PLIP interactions: 2 interactions with chain Y Metal complexes: Y:C.129, Y:C.154 ZN.13: 5 residues within 4Å: Chain 5: C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.71, 5:C.74, 5:C.81, 5:H.84 ZN.14: 6 residues within 4Å: Chain 5: C.111, F.112, C.114, C.154, G.183, C.184 5 PLIP interactions: 5 interactions with chain 5 Metal complexes: 5:C.111, 5:C.114, 5:C.154, 5:G.183, 5:C.184 ZN.17: 4 residues within 4Å: Chain 6: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.1119, 6:C.1122, 6:C.1137, 6:C.1140 ZN.18: 4 residues within 4Å: Chain 7: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.88, 7:C.90, 7:C.94, 7:C.97 ZN.19: 4 residues within 4Å: Chain d: C.17, C.20, C.39, C.42 3 PLIP interactions: 3 interactions with chain d Metal complexes: d:C.17, d:C.20, d:C.42 ZN.20: 4 residues within 4Å: Chain d: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:C.86, d:C.89, d:C.114, d:C.119 ZN.21: 4 residues within 4Å: Chain e: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain e Metal complexes: e:C.7, e:C.10, e:C.44, e:C.45 ZN.22: 5 residues within 4Å: Chain g: C.19, C.22, T.24, C.36, C.39 4 PLIP interactions: 4 interactions with chain g Metal complexes: g:C.19, g:C.22, g:C.36, g:C.39

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

SF4.10: 9 residues within 4Å: Chain H: C.116, I.117, H.118, C.134, C.155, F.157, Y.158, C.190, F.193 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.116, H:C.134, H:C.155, H:C.190

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 4 residues within 4Å: Chain 5: D.495, D.497, D.499 Ligands: ATP-U-C-A-A-C-G2L.2 5 PLIP interactions: 5 interactions with chain 5 Metal complexes: 5:D.495, 5:D.495, 5:D.497, 5:D.497, 5:D.499

1 x W0F: [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

W0F.16: 11 residues within 4Å: Chain 1: C.52, C.53 Chain 5: R.460, D.495, D.497 Chain 6: R.721, Y.724, D.792, K.942, R.975 Ligands: ATP-U-C-A-A-C-G2L.2 5 PLIP interactions: 1 interactions with chain 5, 4 interactions with chain 6 Hydrogen bonds: 5:D.497 Salt bridges: 6:R.721, 6:R.721, 6:K.942, 6:R.975

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structural visualization of transcription initiation in action. Science (2023)

Release Date

2023-12-06

Peptides

CDK-activating kinase assembly factor MAT1: A
General transcription factor IIH subunit 1: B
General transcription factor IIH subunit 2: C
General transcription factor IIH subunit 3: D
General transcription factor IIH subunit 4: E
General transcription factor IIH subunit 5: F
General transcription and DNA repair factor IIH helicase subunit XPB: G
General transcription and DNA repair factor IIH helicase subunit XPD: H
Transcription initiation factor TFIID subunit 1: I
Transcription initiation factor TFIID subunit 2: J
Transcription initiation factor TFIID subunit 4: Kh
Transcription initiation factor TFIID subunit 5: Li
Transcription initiation factor TFIID subunit 6: Mj
Transcription initiation factor TFIID subunit 7: N
Transcription initiation factor TFIID subunit 8: O
Transcription initiation factor TFIID subunit 9: Pk
Transcription initiation factor TFIID subunit 10: Ql
Transcription initiation factor TFIID subunit 12: Rm
Transcription initiation factor IIA subunit 2: S
TATA-box-binding protein: T
Transcription initiation factor IIA beta chain: U
Transcription initiation factor IIB: V
General transcription factor IIF subunit 1: W
General transcription factor IIF subunit 2: X
General transcription factor IIE subunit 1: Y
Transcription initiation factor IIE subunit beta: Z
Transcription initiation factor TFIID subunit 3: 2
Transcription initiation factor TFIID subunit 11: 3
Transcription initiation factor TFIID subunit 13: 4
DNA-directed RNA polymerase subunit: 5
DNA-directed RNA polymerase subunit beta: 6
DNA-directed RNA polymerase II subunit RPB3: 7
DNA-directed RNA polymerase II subunit RPB4: 8
DNA-directed RNA polymerase II subunit E: 9
DNA-directed RNA polymerase II subunit F: a
DNA-directed RNA polymerase II subunit RPB7: b
DNA-directed RNA polymerases I, II, and III subunit RPABC3: c
DNA-directed RNA polymerase II subunit RPB9: d
DNA-directed RNA polymerases I, II, and III subunit RPABC5: e
DNA-directed RNA polymerase II subunit RPB11-a: f
RPB12: g

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
D

h
d

L
E

i
e

M
F

j
f

N
G

O
H

P
I

k
i

Q
J

l
j

R
L

m
l

S
O

T
P

U
Q

V
R

W
S

X
T

Y
U

Z
V

2
c

3
k

4
m

5
o

6
p

7
q

8
r

9
s

a
t

b
u

c
v

d
w

e
x

f
y

g
z

CDK-activating kinase assembly factor MAT1

General transcription factor IIH subunit 1

General transcription factor IIH subunit 2

General transcription factor IIH subunit 3

General transcription factor IIH subunit 4

General transcription factor IIH subunit 5

General transcription and DNA repair factor IIH helicase subunit XPB

General transcription and DNA repair factor IIH helicase subunit XPD

Transcription initiation factor TFIID subunit 1

Transcription initiation factor TFIID subunit 2

Transcription initiation factor TFIID subunit 4

Transcription initiation factor TFIID subunit 5

Transcription initiation factor TFIID subunit 6

Transcription initiation factor TFIID subunit 7

Transcription initiation factor TFIID subunit 8

Transcription initiation factor TFIID subunit 9

Transcription initiation factor TFIID subunit 10

Transcription initiation factor TFIID subunit 12

Transcription initiation factor IIA subunit 2

TATA-box-binding protein

Transcription initiation factor IIA beta chain

Transcription initiation factor IIB

General transcription factor IIF subunit 1

General transcription factor IIF subunit 2

General transcription factor IIE subunit 1

Transcription initiation factor IIE subunit beta

Transcription initiation factor TFIID subunit 3

Transcription initiation factor TFIID subunit 11

Transcription initiation factor TFIID subunit 13

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 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

DNA-directed RNA polymerase II subunit RPB11-a

RPB12

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