SMTL ID : 7ega.1

TFIID-based intermediate PIC on PUMA promoter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain N: C.15, H.18, D.20, C.34, E.36, C.37 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.15, N:H.18, N:C.34, N:E.36 ZN.2: 5 residues within 4Å: Chain Q: C.129, C.132, C.154, C.157, T.159 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.129, Q:C.132, Q:C.154, Q:C.157 ZN.3: 6 residues within 4Å: Chain 1: G.63, C.71, T.73, C.74, C.81, H.84 3 PLIP interactions: 3 interactions with chain 1 Metal complexes: 1:C.71, 1:C.81, 1:H.84 ZN.4: 4 residues within 4Å: Chain 1: C.111, C.114, C.154, C.184 3 PLIP interactions: 3 interactions with chain 1 Metal complexes: 1:C.111, 1:C.114, 1:C.154 ZN.6: 5 residues within 4Å: Chain 2: C.1119, L.1121, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.1119, 2:C.1122, 2:C.1137, 2:C.1140 ZN.7: 4 residues within 4Å: Chain 3: C.90, F.93, C.94, C.97 3 PLIP interactions: 3 interactions with chain 3 Metal complexes: 3:C.90, 3:C.94, 3:C.97 ZN.8: 4 residues within 4Å: Chain 8: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.17, 8:C.20, 8:C.39, 8:C.42 ZN.9: 4 residues within 4Å: Chain 8: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.86, 8:C.89, 8:C.114, 8:C.119 ZN.10: 4 residues within 4Å: Chain 9: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain 9 Metal complexes: 9:C.7, 9:C.10, 9:C.44, 9:C.45 ZN.11: 4 residues within 4Å: Chain b: C.19, C.22, C.36, C.39 3 PLIP interactions: 3 interactions with chain b Metal complexes: b:C.19, b:C.22, b:C.36

1 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structural insights into preinitiation complex assembly on core promoters. Science (2021)

Release Date

2021-05-05

Peptides

Transcription initiation factor TFIID subunit 1: A
Transcription initiation factor TFIID subunit 2: B
Transcription initiation factor TFIID subunit 4: CT
Transcription initiation factor TFIID subunit 5: DU
Transcription initiation factor TFIID subunit 6: EV
Transcription initiation factor TFIID subunit 7: F
Transcription initiation factor TFIID subunit 8: G
Transcription initiation factor TFIID subunit 9: HW
Transcription initiation factor TFIID subunit 10: IX
Transcription initiation factor TFIID subunit 12: JZ
Transcription initiation factor IIA subunit 2: K
TATA-box-binding protein: L
Transcription initiation factor IIA subunit 1: M
Transcription initiation factor IIB: N
General transcription factor IIF subunit 1: O
General transcription factor IIF subunit 2: P
General transcription factor IIE subunit 1: Q
Transcription initiation factor IIE subunit beta: R
Transcription initiation factor TFIID subunit 3: S
Transcription initiation factor TFIID subunit 11: Y
Transcription initiation factor TFIID subunit 13: 0
DNA-directed RNA polymerase subunit: 1
DNA-directed RNA polymerase subunit beta: 2
DNA-directed RNA polymerase II subunit RPB3: 3
DNA-directed RNA polymerase II subunit RPB4: 4
DNA-directed RNA polymerase II subunit E: 5
DNA-directed RNA polymerase II subunit F: 6
DNA-directed RNA polymerases I, II, and III subunit RPABC3: 7
DNA-directed RNA polymerase II subunit RPB9: 8
RPB10: 9
RNA_pol_L_2 domain-containing protein: a
RPB12: b
DNA-directed RNA polymerase II subunit RPB7: e

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

T
d

D
E

U
e

E
F

V
f

F
G

G
H

H
I

W
i

I
J

X
j

J
L

Z
l

K
O

L
P

M
Q

N
R

O
S

P
T

Q
U

R
V

S
c

Y
k

0
m

1
o

2
p

3
q

4
r

5
s

6
t

7
v

8
w

9
x

a
y

b
z

e
u

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 subunit 1

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 polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

RPB10

RNA_pol_L_2 domain-containing protein

RPB12

DNA-directed RNA polymerase II subunit RPB7

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