SMTL ID : 8k5p.1

Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 2 (Pol II Rat1-PTTC2)

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-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.167 ZN.2: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 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: 6 residues within 4Å: Chain G: C.7, D.9, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.29, G:C.32 ZN.7: 5 residues within 4Å: Chain G: C.75, C.78, C.103, S.105, C.106 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.75, G:C.78, G:C.103, G:C.106 ZN.8: 4 residues within 4Å: Chain H: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.45, H:C.46 ZN.9: 4 residues within 4Å: Chain J: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.31, J:C.34, J:C.48, J:C.51

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.481, D.483, D.485 Chain L: A.20 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.481, A:D.481, A:D.483, A:D.483, A:D.485 MG.10: 4 residues within 4Å: Chain Q: K.122, E.218, D.246, D.248 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.246 MG.11: 5 residues within 4Å: Chain R: E.172, D.223, E.241, L.242, K.243 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:D.223, R:E.241, R:L.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, Y. et al., Structural basis of exoribonuclease-mediated mRNA transcription termination. Nature (2024)

Release Date

2024-01-31

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 polymerases I, II, and III subunit RPABC1: D
DNA-directed RNA polymerases I, II, and III subunit RPABC2: E
DNA-directed RNA polymerases I, II, and III subunit RPABC3: F
DNA-directed RNA polymerase II subunit RPB9: G
DNA-directed RNA polymerases I, II, and III subunit RPABC5: H
DNA-directed RNA polymerase II subunit RPB11: I
DNA-directed RNA polymerases I, II, and III subunit RPABC4: J
Transcription elongation factor SPT5: N
DNA-directed RNA polymerase II subunit RPB4: O
DNA-directed RNA polymerase II subunit RPB7: P
5'-3' exoribonuclease 2: Q
Decapping nuclease RAI1: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
H

G
I

H
J

I
K

J
L

N
W

O
D

P
G

Q
M

R
O

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

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

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

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 SPT5

DNA-directed RNA polymerase II subunit RPB4

DNA-directed RNA polymerase II subunit RPB7

5'-3' exoribonuclease 2

Decapping nuclease RAI1

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