SMTL ID : 7nvr.1

Human Mediator with RNA Polymerase II Pre-initiation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Unassigned peptide, likely XPB(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 7 residues within 4Å: Chain H: R.198, L.199, R.200, Q.266, T.267, V.268, S.269 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:V.268 Hydrogen bonds: H:R.198, H:R.198, H:R.198, H:R.200, H:T.267, H:S.269, H:S.269

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

SF4.2: 9 residues within 4Å: Chain A: 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 A, Metal complexes: A:C.116, A:C.134, A:C.155, A:C.190

18 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain D: C.6, C.9, C.31, C.34 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.6, D:C.9, D:C.31, D:C.34 ZN.4: 4 residues within 4Å: Chain D: C.26, H.28, C.46, C.49 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.26, D:H.28, D:H.28, D:C.46, D:C.49 ZN.5: 4 residues within 4Å: Chain E: C.268, C.271, C.282, C.285 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.268, E:C.271, E:C.282, E:C.285 ZN.6: 4 residues within 4Å: Chain E: C.255, C.257, H.258, C.276 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.255, E:C.257, E:H.258, E:H.258, E:C.276 ZN.7: 4 residues within 4Å: Chain G: C.345, C.348, C.368, C.371 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.345, G:C.348, G:C.368, G:C.371 ZN.8: 4 residues within 4Å: Chain G: C.360, C.363, C.382, C.385 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.360, G:C.363, G:C.382, G:C.385 ZN.9: 4 residues within 4Å: Chain G: C.291, C.294, C.305, C.308 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.291, G:C.294, G:C.305, G:C.308 ZN.10: 5 residues within 4Å: Chain K: C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.71, K:C.74, K:C.81, K:H.84 ZN.11: 4 residues within 4Å: Chain K: C.111, C.114, C.154, C.184 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.111, K:C.114, K:C.154, K:C.184 ZN.13: 5 residues within 4Å: Chain L: C.1119, C.1122, C.1137, C.1140, N.1142 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.1119, L:C.1122, L:C.1137, L:C.1140 ZN.14: 4 residues within 4Å: Chain M: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.88, M:C.90, M:C.94, M:C.97 ZN.15: 4 residues within 4Å: Chain S: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.17, S:C.20, S:C.39, S:C.42 ZN.16: 4 residues within 4Å: Chain S: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.86, S:C.89, S:C.114, S:C.119 ZN.17: 5 residues within 4Å: Chain T: C.7, C.10, R.42, C.44, C.45 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.7, T:C.10, T:C.44, T:C.45 ZN.18: 5 residues within 4Å: Chain V: C.19, C.22, C.36, E.38, C.39 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.19, V:C.22, V:C.36, V:C.39 ZN.19: 4 residues within 4Å: Chain W: C.15, H.18, C.34, C.37 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:C.15, W:H.18, W:H.18, W:C.34, W:C.37 ZN.20: 4 residues within 4Å: Chain 4: C.129, C.132, C.154, C.157 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.129, 4:C.132, 4:C.154, 4:C.157 ZN.21: 4 residues within 4Å: Chain m: C.281, C.284, H.306, C.309 4 PLIP interactions: 4 interactions with chain m Metal complexes: m:C.281, m:C.284, m:H.306, m:C.309

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain K: D.495, D.497, D.499 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.495, K:D.495, K:D.497, K:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aibara, S. et al., Structures of mammalian RNA polymerase II pre-initiation complexes. Nature (2021)

Release Date

2021-05-05

Peptides

TFIIH basal transcription factor complex helicase XPD subunit: A
General transcription factor IIH subunit 1: B
General transcription factor IIH subunit 4: C
CDK-activating kinase assembly factor MAT1: D
General transcription factor IIH subunit 3: E
General transcription factor IIH subunit 5: F
General transcription factor IIH subunit 2: G
General transcription and DNA repair factor IIH helicase subunit XPB: H
Cyclin-dependent kinase 7: I
Cyclin-H: J
DNA-directed RNA polymerase subunit: K
DNA-directed RNA polymerase subunit beta: L
DNA-directed RNA polymerase II subunit RPB3: M
RPOL4c domain-containing protein: N
DNA-directed RNA polymerase II subunit E: O
DNA-directed RNA polymerase II subunit F: P
DNA-directed RNA polymerase II subunit RPB7: Q
DNA-directed RNA polymerases I, II, and III subunit RPABC3: R
DNA-directed RNA polymerase II subunit RPB9: S
DNA-directed RNA polymerases I, II, and III subunit RPABC5: T
RNA_pol_L_2 domain-containing protein: U
RNA polymerase II subunit K: V
Transcription initiation factor IIB: W
TATA-box-binding protein: Y
General transcription factor IIF subunit 1: Z
General transcription factor IIF subunit 2: 0
Transcription initiation factor IIA subunit 1: 2
Transcription initiation factor IIA subunit 2: 3
General transcription factor IIE subunit 1: 4
Transcription initiation factor IIE subunit beta: 5
Unassigned peptide, likely TFIIE-beta: 6
Mediator of RNA polymerase II transcription subunit 6: 7
Mediator of RNA polymerase II transcription subunit 8: 8
Mediator of RNA polymerase II transcription subunit 11: 9
Mediator of RNA polymerase II transcription subunit 17: a
Mediator of RNA polymerase II transcription subunit 18: b
Mediator of RNA polymerase II transcription subunit 20: c
Mediator of RNA polymerase II transcription subunit 22: d
Mediator of RNA polymerase II transcription subunit 4: e
Mediator of RNA polymerase II transcription subunit 7: f
Mediator of RNA polymerase II transcription subunit 9: g
Mediator of RNA polymerase II transcription subunit 10: h
Mediator of RNA polymerase II transcription subunit 14: i
Mediator of RNA polymerase II transcription subunit 19: j
Mediator of RNA polymerase II transcription subunit 21: k
Mediator of RNA polymerase II transcription subunit 31: l
Mediator of RNA polymerase II transcription subunit 27: m
Mediator of RNA polymerase II transcription subunit 28: n
unassigned peptide (MED29 or MED30): o
Mediator of RNA polymerase II transcription subunit 30: p
unassigned peptide (MED14): q
unassigned peptide (MED6): r
unassigned peptide (MED17): s
unassigned peptide (MED29 or MED30): t
unassigned peptide (MED29 or MED30): u

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
C

N
D

O
E

P
F

Q
G

R
H

S
I

T
J

U
K

V
L

W
M

Y
O

Z
Q

0
R

2
U

3
V

4
W

5
X

6
Y

7
a

8
b

9
c

a
d

b
e

c
f

d
g

e
h

f
i

g
j

h
k

i
l

j
m

k
n

l
o

m
p

n
q

o
r

p
s

q
v

r
w

s
x

t
y

u
z

TFIIH basal transcription factor complex helicase XPD subunit

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4

CDK-activating kinase assembly factor MAT1

General transcription factor IIH subunit 3

General transcription factor IIH subunit 5

General transcription factor IIH subunit 2

General transcription and DNA repair factor IIH helicase subunit XPB

Cyclin-dependent kinase 7

Cyclin-H

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RPOL4c domain-containing protein

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

RNA_pol_L_2 domain-containing protein

RNA polymerase II subunit K

Transcription initiation factor IIB

TATA-box-binding protein

General transcription factor IIF subunit 1

General transcription factor IIF subunit 2

Transcription initiation factor IIA subunit 1

Transcription initiation factor IIA subunit 2

General transcription factor IIE subunit 1

Transcription initiation factor IIE subunit beta

Unassigned peptide, likely TFIIE-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 27

Mediator of RNA polymerase II transcription subunit 28

unassigned peptide (MED29 or MED30)

Mediator of RNA polymerase II transcription subunit 30

unassigned peptide (MED14)

unassigned peptide (MED6)

unassigned peptide (MED17)

unassigned peptide (MED29 or MED30)

unassigned peptide (MED29 or MED30)

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