SMTL ID : 9eh1.1

RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.62, C.65, C.72, P.73, H.75 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.62, A:C.65, A:C.72, A:H.75 ZN.2: 3 residues within 4Å: Chain A: N.143, G.174, R.177 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.143 ZN.4: 4 residues within 4Å: Chain B: C.1104, C.1107, C.1122, C.1125 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1104, B:C.1107, B:C.1122, B:C.1125 ZN.5: 4 residues within 4Å: Chain C: C.87, C.89, C.93, C.96 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.87, C:C.89, C:C.96 ZN.6: 5 residues within 4Å: Chain I: C.8, C.11, C.30, C.33, Y.35 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.8, I:C.11, I:C.30 ZN.7: 4 residues within 4Å: Chain I: C.77, C.80, C.105, C.110 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.77, I:C.80, I:C.105, I:C.110 ZN.8: 4 residues within 4Å: Chain J: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.44, J:C.44, J:C.45 ZN.9: 6 residues within 4Å: Chain L: R.24, C.25, R.26, E.27, G.29, Y.30 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:C.25, L:E.27 ZN.10: 5 residues within 4Å: Chain Y: C.15, L.17, C.18, S.19, C.32 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:C.18

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.486, D.488, D.490 Chain P: C.11 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.488, A:D.488

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Markert, J.W. et al., Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription. Science (2024)

Release Date

2024-12-18

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
RNA polymerase Rpb4/RPC9 core 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 subunit: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerase I, II, and III subunit RPABC5: J
DNA-directed RNA polymerase II subunit RPB11-a: K
RNA polymerase II subunit K: L
Transcription elongation factor SPT6: M
Protein IWS1 homolog: O
RNA polymerase-associated protein CTR9 homolog: Q
RNA polymerase-associated protein RTF1 homolog: R
Transcription elongation factor A protein 1: S
RNA polymerase-associated protein LEO1: U
RNA polymerase II-associated factor 1 homolog: V
Superkiller complex protein 8, N-terminally processed: W
Parafibromin: X
Transcription elongation factor SPT4: Y
Transcription elongation factor SPT5: Z
Histone H3: 04
Histone H4: 15
Histone H2A type 1: 26
Histone H2B 1.1: 37
Histone-lysine N-methyltransferase SETD2: 8

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

S
S

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

4
e

1
b

5
f

2
c

6
g

3
d

7
h

8
l

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RNA polymerase Rpb4/RPC9 core domain-containing protein

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerase I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11-a

RNA polymerase II subunit K

Transcription elongation factor SPT6

Protein IWS1 homolog

RNA polymerase-associated protein CTR9 homolog

RNA polymerase-associated protein RTF1 homolog

Transcription elongation factor A protein 1

RNA polymerase-associated protein LEO1

RNA polymerase II-associated factor 1 homolog

Superkiller complex protein 8, N-terminally processed

Parafibromin

Transcription elongation factor SPT4

Transcription elongation factor SPT5

Histone H3

Histone H4

Histone H2A type 1

Histone H2B 1.1

Histone-lysine N-methyltransferase SETD2

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