SMTL ID : 9s3g.1

State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: 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.154, G.183, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154, A:C.184 ZN.4: 4 residues within 4Å: Chain B: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1119, B:C.1122, B:C.1137, B:C.1140 ZN.5: 5 residues within 4Å: Chain C: C.88, C.90, C.94, E.96, C.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.94, C:E.96 ZN.6: 4 residues within 4Å: Chain I: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 ZN.7: 4 residues within 4Å: Chain I: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 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.10, J:C.44, J:C.45 ZN.9: 6 residues within 4Å: Chain L: C.19, C.22, C.36, E.38, C.39, Y.41 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.19, L:C.22, L:C.36, L:E.38, L:C.39 ZN.10: 4 residues within 4Å: Chain Y: C.20, C.23, C.37, C.40 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.20, Y:C.23, Y:C.37, Y:C.40

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain P: A.21 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.495, A:D.495, A:D.497, A:D.497, A:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walshe, J.L. et al., Molecular mechanism of co-transcriptional H3K36 methylation by SETD2. Nat Commun (2025)

Release Date

2025-11-12

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
Transcription elongation factor SPT6: M
Histone-lysine N-methyltransferase SETD2: 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
WD repeat-containing protein 61: W
Parafibromin: X
Transcription elongation factor SPT4: Y
Transcription elongation factor SPT5: Z
Histone H3.2: 02
Histone H4: 13
Histone H2A type 1-B/E: 4
Histone H2B type 1-K: 5
FACT complex subunit SPT16: 6
FACT complex subunit SSRP1: 7

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

2
e

1
b

3
f

4
g

5
h

6
j

7
k

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

Transcription elongation factor SPT6

Histone-lysine N-methyltransferase SETD2

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

WD repeat-containing protein 61

Parafibromin

Transcription elongation factor SPT4

Transcription elongation factor SPT5

Histone H3.2

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-K

FACT complex subunit SPT16

FACT complex subunit SSRP1

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