SMTL ID : 7und.1

Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: G.63, C.71, C.74, C.81, P.82, H.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.74, A:C.81, A:H.84 ZN.2: 5 residues within 4Å: Chain A: C.111, C.114, C.184, G.185, R.186 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.114, A:C.184 ZN.4: 7 residues within 4Å: Chain B: C.1196, L.1198, C.1199, G.1200, I.1201, C.1214, C.1217 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1196, B:C.1199, B:C.1214, B:C.1217 ZN.5: 6 residues within 4Å: Chain C: C.88, C.90, F.93, C.94, C.97 Chain Y: K.718 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.97 ZN.6: 7 residues within 4Å: Chain I: C.17, C.20, N.22, L.24, C.39, C.42, Y.44 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39 ZN.7: 7 residues within 4Å: Chain I: C.86, C.89, G.90, H.91, C.114, C.119, H.121 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.8: 7 residues within 4Å: Chain J: C.7, T.9, C.10, R.42, C.44, C.45, R.47 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.44, J:C.45 ZN.9: 1 residues within 4Å: Chain R: F.490 No protein-ligand interaction detected (PLIP) ZN.10: 6 residues within 4Å: Chain X: C.16, L.18, C.19, S.20, C.33, N.35 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:C.19

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain P: G.18 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.497, A:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filipovski, M. et al., Structural basis of nucleosome retention during transcription elongation. Science (2022)

Release Date

2022-10-19

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
RPOL4c domain-containing protein: D
DNA-directed RNA polymerase II subunit E: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2: F
DNA-directed RNA polymerase II subunit RPB7: G
RPB8: H
RPB9: I
RPB10: J
RPB11: K
RNA polymerase II subunit K: L
Transcription elongation factor SPT6: M
Transcription elongation factor A protein 1: O
RNA polymerase-associated protein CTR9 homolog: Q
RNA polymerase-associated protein RTF1 homolog: R
RNA polymerase-associated protein LEO1: T
RNA polymerase II-associated factor 1 homolog: U
WDR61: V
Parafibromin: W
Transcription elongation factor SPT4: X
Transcription elongation factor SPT5: Y
Histone H3.2: Z3
Histone H4: 04
Histone H2A: 15
Histone H2B 1.1: 26

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

O
O

Q
Q

R
R

T
U

U
V

V
W

W
X

X
Y

Y
Z

Z
a

3
e

0
b

4
f

1
c

5
g

2
d

6
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 polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase II subunit RPB7

RPB8

RPB9

RPB10

RPB11

RNA polymerase II subunit K

Transcription elongation factor SPT6

Transcription elongation factor A protein 1

RNA polymerase-associated protein CTR9 homolog

RNA polymerase-associated protein RTF1 homolog

RNA polymerase-associated protein LEO1

RNA polymerase II-associated factor 1 homolog

WDR61

Parafibromin

Transcription elongation factor SPT4

Transcription elongation factor SPT5

Histone H3.2

Histone H4

Histone H2A

Histone H2B 1.1

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