SMTL ID : 7lbm.1

Structure of the human Mediator-bound transcription pre-initiation complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain E: R.460, N.493, D.495, D.499 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.495 MG.4: 3 residues within 4Å: Chain E: A.494, D.495 Chain F: E.791 No protein-ligand interaction detected (PLIP)

16 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain E: C.71, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.71, E:C.74, E:C.81, E:H.84 ZN.3: 3 residues within 4Å: Chain E: C.111, C.114, C.184 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.111, E:C.114, E:C.184 ZN.5: 4 residues within 4Å: Chain F: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.1119, F:C.1122, F:C.1137, F:C.1140 ZN.6: 5 residues within 4Å: Chain G: C.88, C.90, F.93, C.94, C.97 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.88, G:C.90, G:C.94, G:C.97 ZN.7: 5 residues within 4Å: Chain M: C.17, E.19, C.20, N.21, C.42 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.17, M:C.20, M:C.42 ZN.8: 4 residues within 4Å: Chain M: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.86, M:C.89, M:C.114, M:C.119 ZN.9: 4 residues within 4Å: Chain N: C.7, C.10, C.44, C.45 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:C.7, N:C.10, N:C.44 ZN.10: 5 residues within 4Å: Chain P: C.19, C.22, C.36, R.37, C.39 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:C.19, P:C.22, P:C.36 ZN.11: 4 residues within 4Å: Chain S: C.15, H.18, C.34, C.37 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:C.15, S:H.18, S:C.34 ZN.12: 5 residues within 4Å: Chain U: C.129, V.131, C.132, C.154, C.157 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:C.129, U:C.154 ZN.14: 4 residues within 4Å: Chain 4: C.345, C.348, C.368, C.371 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.345, 4:C.348, 4:C.368, 4:C.371 ZN.15: 4 residues within 4Å: Chain 4: C.360, C.363, C.382, C.385 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.360, 4:C.363, 4:C.382, 4:C.385 ZN.16: 5 residues within 4Å: Chain 4: C.291, Q.293, C.294, C.305, C.308 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.291, 4:C.294, 4:C.305, 4:C.308 ZN.17: 5 residues within 4Å: Chain 5: C.268, C.271, C.282, C.285, T.287 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.268, 5:C.271, 5:C.282, 5:C.285 ZN.18: 5 residues within 4Å: Chain 7: C.6, C.9, C.31, S.33, C.34 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.6, 7:C.9, 7:C.31, 7:C.34 ZN.19: 4 residues within 4Å: Chain 7: C.26, H.28, C.46, C.49 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.26, 7:H.28, 7:C.46, 7:C.49

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

SF4.13: 9 residues within 4Å: Chain 1: C.116, H.118, V.121, C.134, T.138, C.155, F.157, Y.158, C.190 5 PLIP interactions: 5 interactions with chain 1, Salt bridges: 1:D.302 Metal complexes: 1:C.116, 1:C.134, 1:C.155, 1:C.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abdella, R. et al., Structure of the human Mediator-bound transcription preinitiation complex. Science (2021)

Release Date

2021-03-24

Peptides

Isoform 2 of Mediator of RNA polymerase II transcription subunit 16: A
Mediator of RNA polymerase II transcription subunit 23: B
Mediator of RNA polymerase II transcription subunit 24: C
Mediator of RNA polymerase II transcription subunit 25: D
DNA-directed RNA polymerase II subunit RPB1: E
DNA-directed RNA polymerase II subunit RPB2: F
DNA-directed RNA polymerase II subunit RPB3: G
DNA-directed RNA polymerase II subunit RPB4: H
DNA-directed RNA polymerase II subunit RPB5: I
DNA-directed RNA polymerases I, II, and III subunit RPABC2: J
DNA-directed RNA polymerase II subunit RPB7: K
DNA-directed RNA polymerases I, II, and III subunit RPABC3: L
DNA-directed RNA polymerase II subunit RPB9: M
DNA-directed RNA polymerases I, II, and III subunit RPABC5: N
DNA-directed RNA polymerase II subunit RPB11-a: O
DNA-directed RNA polymerases I, II, and III subunit RPABC4: P
Transcription initiation factor IIA subunit 1: Q
Transcription initiation factor IIA subunit 2: R
Transcription initiation factor IIB: S
TATA-box-binding protein: T
General transcription factor IIE subunit 1: U
Transcription initiation factor IIE subunit beta: V
General transcription factor IIF subunit 1: W
General transcription factor IIF subunit 2: X
TFIIH basal transcription factor complex helicase XPB subunit: 0
TFIIH basal transcription factor complex helicase XPD subunit: 1
General transcription factor IIH subunit 1: 2
General transcription factor IIH subunit 4, p52: 3
General transcription factor IIH subunit 2: 4
General transcription factor IIH subunit 3: 5
General transcription factor IIH subunit 5: 6
CDK-activating kinase assembly factor MAT1: 7
Cyclin-dependent kinase 7: 8
Cyclin-H: 9
Mediator of RNA polymerase II transcription subunit 6: a
Mediator of RNA polymerase II transcription subunit 8: b
Mediator of RNA polymerase II transcription subunit 11: c
Mediator of RNA polymerase II transcription subunit 17: d
Mediator of RNA polymerase II transcription subunit 18: e
Mediator of RNA polymerase II transcription subunit 20: f
Mediator of RNA polymerase II transcription subunit 22: g
Mediator of RNA polymerase II transcription subunit 27: h
Mediator of RNA polymerase II transcription subunit 28: i
Mediator of RNA polymerase II transcription subunit 29: j
Mediator of RNA polymerase II transcription subunit 30: k
Mediator of RNA polymerase II transcription subunit 14: l
Mediator of RNA polymerase II transcription subunit 4: m
Mediator of RNA polymerase II transcription subunit 7: n
Mediator of RNA polymerase II transcription subunit 9: o
Mediator of RNA polymerase II transcription subunit 10: p
Mediator of RNA polymerase II transcription subunit 19: q
Mediator of RNA polymerase II transcription subunit 21: r
Mediator of RNA polymerase II transcription subunit 31: s
Mediator of RNA polymerase II transcription subunit 15: t

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
2

D
3

E
A

F
B

G
C

H
D

I
E

J
F

K
G

L
H

M
I

N
J

O
K

P
L

Q
M

R
N

S
O

T
P

U
Q

V
R

W
S

X
T

0
W

1
X

2
Y

3
Z

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
q

l
r

m
s

n
t

o
u

p
v

q
w

r
x

s
y

t
z

Isoform 2 of Mediator of RNA polymerase II transcription subunit 16

Mediator of RNA polymerase II transcription subunit 23

Mediator of RNA polymerase II transcription subunit 24

Mediator of RNA polymerase II transcription subunit 25

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 polymerase II subunit RPB5

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-a

DNA-directed RNA polymerases I, II, and III subunit RPABC4

Transcription initiation factor IIA subunit 1

Transcription initiation factor IIA subunit 2

Transcription initiation factor IIB

TATA-box-binding protein

General transcription factor IIE subunit 1

Transcription initiation factor IIE subunit beta

General transcription factor IIF subunit 1

General transcription factor IIF subunit 2

TFIIH basal transcription factor complex helicase XPB subunit

TFIIH basal transcription factor complex helicase XPD subunit

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4, p52

General transcription factor IIH subunit 2

General transcription factor IIH subunit 3

General transcription factor IIH subunit 5

CDK-activating kinase assembly factor MAT1

Cyclin-dependent kinase 7

Cyclin-H

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 27

Mediator of RNA polymerase II transcription subunit 28

Mediator of RNA polymerase II transcription subunit 29

Mediator of RNA polymerase II transcription subunit 30

Mediator of RNA polymerase II transcription subunit 14

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 19

Mediator of RNA polymerase II transcription subunit 21

Mediator of RNA polymerase II transcription subunit 31

Mediator of RNA polymerase II transcription subunit 15

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