SMTL ID : 8ceo.1

Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: C.115, L.116, H.117, V.120, C.133, C.156, Y.158, 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: 5 residues within 4Å: Chain D: C.13, C.16, C.39, S.41, C.42 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.13, D:C.16, D:C.39, D:C.42 ZN.3: 4 residues within 4Å: Chain D: C.34, H.36, C.54, C.59 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.34, D:H.36, D:C.54, D:C.59 ZN.4: 4 residues within 4Å: Chain E: C.289, C.292, C.305, C.308 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.289, E:C.292, E:C.305, E:C.308 ZN.5: 5 residues within 4Å: Chain G: C.349, C.352, S.354, C.363, C.366 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.349, G:C.352, G:C.363, G:C.366 ZN.6: 4 residues within 4Å: Chain G: C.403, C.406, C.437, C.440 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.403, G:C.406, G:C.437, G:C.440 ZN.7: 4 residues within 4Å: Chain G: C.429, C.432, C.451, C.454 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.429, G:C.432, G:C.451, G:C.454 ZN.8: 4 residues within 4Å: Chain G: C.336, C.338, H.339, C.357 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.336, G:C.338, G:H.339, G:C.357 ZN.9: 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.10: 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.12: 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.13: 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.14: 5 residues within 4Å: Chain Q: C.7, C.10, C.29, T.31, C.32 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:C.7, Q:C.10, Q:C.29, Q:T.31, Q:C.32 ZN.15: 5 residues within 4Å: Chain Q: C.75, C.78, C.103, S.105, 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.16: 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.17: 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.18: 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.19: 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 MG: MAGNESIUM ION(Non-covalent)

MG.11: 3 residues within 4Å: Chain I: D.481, D.483, D.485 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.483, I:D.483, I:D.485, I:D.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schilbach, S. et al., Yeast PIC-Mediator structure with RNA polymerase II C-terminal domain. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-03-08

Peptides

General transcription and DNA repair factor IIH helicase subunit XPD: A
TFB1 isoform 1: B
RNA polymerase II transcription factor B subunit 2: 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: 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-binding protein: W
Transcription initiation factor IIF subunit alpha: X
Transcription initiation factor IIF subunit beta: Y
TOA1 isoform 1: 0
Transcription initiation factor IIA subunit 2: 1
Transcription initiation factor IIE subunit alpha: 2
Transcription initiation factor IIE subunit beta: 3
Mediator of RNA polymerase II transcription subunit 6: 4
Mediator of RNA polymerase II transcription subunit 8: 5
Mediator of RNA polymerase II transcription subunit 11: 6
Mediator of RNA polymerase II transcription subunit 17: 7
Mediator of RNA polymerase II transcription subunit 18: 8
Mediator of RNA polymerase II transcription subunit 20: 9
Mediator of RNA polymerase II transcription subunit 22: a
Mediator of RNA polymerase II transcription subunit 4: b
Mediator of RNA polymerase II transcription subunit 7: c
Mediator of RNA polymerase II transcription subunit 9: d
Mediator of RNA polymerase II transcription subunit 10: e
Mediator of RNA polymerase II transcription subunit 14: f
Mediator of RNA polymerase II transcription subunit 19: g
Mediator of RNA polymerase II transcription subunit 21: h
Mediator of RNA polymerase II transcription subunit 31: i
Mediator of RNA polymerase II transcription subunit 1: j
Histone H3.2: ko
Histone H4: lp
Histone H2A: mq
Histone H2B: nr

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
a

5
b

6
c

7
d

8
e

9
f

a
g

b
h

c
i

d
j

e
k

f
l

g
m

h
n

i
o

j
p

k
r

o
v

l
s

p
w

m
t

q
x

n
u

r
y

General transcription and DNA repair factor IIH helicase subunit XPD

TFB1 isoform 1

RNA polymerase II transcription factor B subunit 2

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

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-binding protein

Transcription initiation factor IIF subunit alpha

Transcription initiation factor IIF subunit beta

TOA1 isoform 1

Transcription initiation factor IIA subunit 2

Transcription initiation factor IIE subunit alpha

Transcription initiation factor IIE subunit beta

Mediator of RNA polymerase II transcription subunit 6

Mediator of RNA polymerase II transcription subunit 8

Mediator of RNA polymerase II transcription subunit 11

Mediator of RNA polymerase II transcription subunit 17

Mediator of RNA polymerase II transcription subunit 18

Mediator of RNA polymerase II transcription subunit 20

Mediator of RNA polymerase II transcription subunit 22

Mediator of RNA polymerase II transcription subunit 4

Mediator of RNA polymerase II transcription subunit 7

Mediator of RNA polymerase II transcription subunit 9

Mediator of RNA polymerase II transcription subunit 10

Mediator of RNA polymerase II transcription subunit 14

Mediator of RNA polymerase II transcription subunit 19

Mediator of RNA polymerase II transcription subunit 21

Mediator of RNA polymerase II transcription subunit 31

Mediator of RNA polymerase II transcription subunit 1

Histone H3.2

Histone H4

Histone H2A

Histone H2B

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