SMTL ID : 8rap.1

Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex

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-mer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.107, H.109, C.110, C.167 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.167 ZN.2: 4 residues within 4Å: Chain A: G.59, C.67, C.77, H.80 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.67, A:C.77 ZN.4: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.5: 4 residues within 4Å: Chain C: C.86, C.88, C.92, C.95 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.86, C:C.88, C:C.92, C:C.95 ZN.6: 3 residues within 4Å: Chain I: C.7, C.29, C.32 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.7, I:C.32 ZN.7: 5 residues within 4Å: Chain I: C.75, C.78, C.103, S.105, C.106 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103, I:C.106 ZN.8: 4 residues within 4Å: Chain J: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45, J:C.46 ZN.9: 4 residues within 4Å: Chain L: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51 ZN.10: 4 residues within 4Å: Chain M: C.25, C.28, C.49, C.52 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.25, M:C.28, M:C.49, M:C.52

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.481, D.483 Chain P: U.35 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.483 MG.12: 4 residues within 4Å: Chain O: K.1363, T.1364 Ligands: ADP.11, BEF.13 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.1364

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 17 residues within 4Å: Chain O: K.1334, P.1359, G.1360, T.1361, G.1362, K.1363, T.1364, K.1365, R.1422, Y.1655, R.1656, G.1785, Q.1786, E.1787, R.1820 Ligands: MG.12, BEF.13 16 PLIP interactions: 16 interactions with chain O Hydrogen bonds: O:K.1334, O:G.1360, O:G.1362, O:K.1363, O:T.1364, O:T.1364, O:K.1365, O:R.1422, O:R.1422, O:E.1787 Salt bridges: O:R.1656, O:R.1656, O:R.1820 pi-Stacking: O:Y.1655 pi-Cation interactions: O:K.1365, O:K.1365

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.13: 10 residues within 4Å: Chain O: P.1358, P.1359, K.1363, E.1591, Q.1619, R.1656, G.1785, R.1820 Ligands: ADP.11, MG.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rengachari, S. et al., Mechanism of polyadenylation-independent RNA polymerase II termination. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-10-30

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase II subunit RPB2: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerase II subunit RPB4: D
DNA-directed RNA polymerases I, II, and III subunit RPABC1: 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: K
DNA-directed RNA polymerases I, II, and III subunit RPABC4: L
Transcription elongation factor 1: M
Helicase SEN1: O
Transcription elongation factor SPT4: R
Transcription elongation factor SPT5: S

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

R
Y

S
Z

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit RPB4

DNA-directed RNA polymerases I, II, and III subunit RPABC1

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

DNA-directed RNA polymerases I, II, and III subunit RPABC4

Transcription elongation factor 1

Helicase SEN1

Transcription elongation factor SPT4

Transcription elongation factor SPT5

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