SMTL ID : 8bvw.1

RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-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: 5 residues within 4Å: Chain A: R.198, Q.266, T.267, V.268, S.269 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.268 Hydrogen bonds: A:R.198, A:Q.266, A:S.269

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

SF4.2: 10 residues within 4Å: Chain B: C.116, I.117, H.118, C.134, C.155, F.157, Y.158, C.190, Y.192, F.193 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.116, B:C.134, B:C.155, B:C.190

17 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain E: C.345, C.348, C.368, C.371 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.345, E:C.348, E:C.368, E:C.371 ZN.4: 3 residues within 4Å: Chain E: F.331, C.360, C.382 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:C.360, E:C.382 ZN.5: 4 residues within 4Å: Chain E: C.291, C.294, C.305, C.308 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.291, E:C.294, E:C.305, E:C.308 ZN.6: 3 residues within 4Å: Chain F: C.268, C.271, C.282 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.268, F:C.271, F:C.282 ZN.7: 2 residues within 4Å: Chain F: H.258, C.276 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.258, F:H.258, F:C.276 ZN.8: 4 residues within 4Å: Chain H: C.6, R.8, L.30, C.34 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:C.6, H:C.34 ZN.9: 3 residues within 4Å: Chain H: C.26, G.27, C.49 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:C.26, H:C.26 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: 3 residues within 4Å: Chain K: C.111, C.114, C.154 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.111, K:C.114, K:C.154 ZN.13: 4 residues within 4Å: Chain L: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.1119, L:C.1122, L:C.1137, L:C.1140 ZN.14: 6 residues within 4Å: Chain M: C.88, C.90, E.92, F.93, C.94, C.97 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.90, M:E.92, 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: 4 residues within 4Å: Chain T: C.7, C.10, 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 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:C.19, V:C.22, V:C.36 ZN.19: 4 residues within 4Å: Chain W: N.17, H.18, C.34, C.37 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:H.18, W:H.18, W:C.34 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain K: D.495, D.497, D.499 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:D.495, K:D.497, K:D.497, K:D.499, K:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abril-Garrido, J. et al., Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Mol.Cell (2023)

Release Date

2023-05-03

Peptides

General transcription and DNA repair factor IIH helicase subunit XPB: A
TFIIH basal transcription factor complex helicase XPD subunit: B
General transcription factor IIH subunit 1: C
General transcription factor IIH subunit 4: D
General transcription factor IIH subunit 2: E
General transcription factor IIH subunit 3: F
General transcription factor IIH subunit 5: G
CDK-activating kinase assembly factor MAT1: 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
RNA polymerase II subunit D: 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
DNA-directed RNA polymerase II subunit RPB11-a: 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
Histone H3.2: 7b
Histone H4: 8c
Histone H2A type 1: 9d
Histone H2B 1.1: ae

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
Z

7
a

b
e

8
b

c
f

9
c

d
g

a
d

e
h

General transcription and DNA repair factor IIH helicase subunit XPB

TFIIH basal transcription factor complex helicase XPD subunit

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4

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

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RNA polymerase II subunit D

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

DNA-directed RNA polymerase II subunit RPB11-a

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

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

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