SMTL ID : 7egc.1

p53-bound TFIID-based holo PIC on HDM2 promoter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.6, C.9, C.31, S.33, C.34 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.6, A:C.9, A:C.31, A:C.34 ZN.2: 5 residues within 4Å: Chain A: C.26, C.46, C.49, G.50, T.51 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.46 ZN.3: 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.4: 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.5: 5 residues within 4Å: Chain C: C.291, Q.293, 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.6: 5 residues within 4Å: Chain D: C.268, C.271, C.282, C.285, T.287 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.268, D:C.271, D:C.282, D:C.285 ZN.8: 5 residues within 4Å: Chain X: C.15, H.18, C.34, E.36, C.37 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.15, X:H.18, X:C.34, X:C.37 ZN.9: 5 residues within 4Å: Chain 0: C.129, C.132, C.154, C.157, T.159 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.129, 0:C.132, 0:C.154, 0:C.157 ZN.10: 6 residues within 4Å: Chain d: G.63, C.71, T.73, C.74, C.81, H.84 3 PLIP interactions: 3 interactions with chain d Metal complexes: d:C.71, d:C.81, d:H.84 ZN.11: 4 residues within 4Å: Chain d: C.111, C.114, C.154, C.184 3 PLIP interactions: 3 interactions with chain d Metal complexes: d:C.111, d:C.114, d:C.154 ZN.13: 5 residues within 4Å: Chain e: C.1119, L.1121, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain e Metal complexes: e:C.1119, e:C.1122, e:C.1137, e:C.1140 ZN.14: 4 residues within 4Å: Chain f: C.90, F.93, C.94, C.97 3 PLIP interactions: 3 interactions with chain f Metal complexes: f:C.90, f:C.94, f:C.97 ZN.15: 4 residues within 4Å: Chain l: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain l Metal complexes: l:C.17, l:C.20, l:C.39, l:C.42 ZN.16: 4 residues within 4Å: Chain l: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain l Metal complexes: l:C.86, l:C.89, l:C.114, l:C.119 ZN.17: 4 residues within 4Å: Chain m: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain m Metal complexes: m:C.7, m:C.10, m:C.44, m:C.45 ZN.18: 4 residues within 4Å: Chain o: C.19, C.22, C.36, C.39 3 PLIP interactions: 3 interactions with chain o Metal complexes: o:C.19, o:C.22, o:C.36

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

SF4.7: 9 residues within 4Å: Chain H: C.116, H.118, V.121, C.134, T.138, C.155, F.157, Y.158, C.190 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.12: 3 residues within 4Å: Chain d: D.495, D.497, D.499 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:D.495, d:D.495, d:D.497, d: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

2021-05-12

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
Cyclin-dependent kinase 7: I
Cyclin-H: J
Transcription initiation factor TFIID subunit 1: K
Transcription initiation factor TFIID subunit 2: L
Transcription initiation factor TFIID subunit 4: M5
Transcription initiation factor TFIID subunit 5: N6
Transcription initiation factor TFIID subunit 6: O7
Transcription initiation factor TFIID subunit 7: P
Transcription initiation factor TFIID subunit 8: Q
Transcription initiation factor TFIID subunit 9: R8
Transcription initiation factor TFIID subunit 10: S9
Transcription initiation factor TFIID subunit 12: Tb
Transcription initiation factor IIA subunit 2: U
TATA-box-binding protein: V
Transcription initiation factor IIA subunit 1: W
Transcription initiation factor IIB: X
General transcription factor IIF subunit 1: Y
General transcription factor IIF subunit 2: Z
General transcription factor IIE subunit 1: 0
Transcription initiation factor IIE subunit beta: 1
Transcription initiation factor TFIID subunit 3: 4
Transcription initiation factor TFIID subunit 11: a
Transcription initiation factor TFIID subunit 13: c
DNA-directed RNA polymerase II subunit RPB1: d
DNA-directed RNA polymerase subunit beta: e
DNA-directed RNA polymerase II subunit RPB3: f
DNA-directed RNA polymerase II subunit RPB4: g
DNA-directed RNA polymerase II subunit E: h
DNA-directed RNA polymerase II subunit F: i
DNA-directed RNA polymerase II subunit RPB7: j
DNA-directed RNA polymerases I, II, and III subunit RPABC3: k
DNA-directed RNA polymerase II subunit RPB9: l
RPB10: m
RNA_pol_L_2 domain-containing protein: n
RPB12: o

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
8

J
9

K
A

L
B

M
D

5
d

N
E

6
e

O
F

7
f

P
G

Q
H

R
I

8
i

S
J

9
j

T
L

b
l

U
O

V
P

W
Q

X
R

Y
S

Z
T

0
U

1
V

4
c

a
k

c
m

d
o

e
p

f
q

g
r

h
s

i
t

j
u

k
v

l
w

m
x

n
y

o
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

Cyclin-dependent kinase 7

Cyclin-H

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 II subunit RPB1

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

RPB10

RNA_pol_L_2 domain-containing protein

RPB12

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