SMTL ID : 8a3y.1

Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: G.63, C.71, T.73, C.74, C.81, P.82, H.84 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.71, A:C.74, A:H.84 ZN.2: 6 residues within 4Å: Chain A: C.111, L.118, N.152, G.183, R.186, Q.188 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.152 ZN.3: 5 residues within 4Å: Chain B: C.1196, L.1198, C.1199, C.1214, C.1217 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1196, B:C.1199, B:C.1214 ZN.4: 5 residues within 4Å: Chain C: C.88, C.90, F.93, C.94, C.97 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.97 ZN.5: 7 residues within 4Å: Chain I: C.17, E.19, C.20, N.22, 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.6: 8 residues within 4Å: Chain I: C.86, C.89, G.90, H.91, C.114, A.116, 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.7: 8 residues within 4Å: Chain J: C.7, T.9, C.10, G.11, K.12, R.42, C.44, C.45 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.7, J:C.44, J:C.45 ZN.8: 5 residues within 4Å: Chain L: R.35, C.36, C.39, G.40, Y.41 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:C.36 ZN.10: 5 residues within 4Å: Chain W: C.20, L.22, C.23, S.24, C.37 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:C.23

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 5 residues within 4Å: Chain A: D.495, D.497, D.499 Chain O: U.21, C.22 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farnung, L. et al., Structure of a backtracked hexasomal intermediate of nucleosome transcription. Mol.Cell (2022)

Release Date

2024-07-31

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
RNA polymerase II subunit D: 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
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5: J
DNA-directed RNA polymerase II subunit RPB11-a: K
RNA polymerase II subunit K: L
SPT6: M
RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein LEO1: PS
RNA polymerase-associated protein RTF1 homolog: Q
RNA polymerase II-associated factor 1 homolog: T
WD repeat-containing protein 61: U
Parafibromin: V
Transcription elongation factor SPT4: W
Transcription elongation factor SPT5: X
Histone H3.2: Y2
Histone H4: Z3
Histone H2A: 0
Histone H2B: 1

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

P
Q

S
U

Q
R

T
V

U
W

V
X

W
Y

X
Z

Y
a

2
e

Z
b

3
f

0
c

1
d

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 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

RNA polymerase II subunit K

SPT6

RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein LEO1

RNA polymerase-associated protein RTF1 homolog

RNA polymerase II-associated factor 1 homolog

WD repeat-containing protein 61

Parafibromin

Transcription elongation factor SPT4

Transcription elongation factor SPT5

Histone H3.2

Histone H4

Histone H2A

Histone H2B

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