SMTL ID : 7oq4.1

Cryo-EM structure of the ATV RNAP Inhibitory Protein (RIP) bound to the DNA-binding channel of the host's RNA polymerase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.456, D.458, D.460 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.456, A:D.456, A:D.458, A:D.460, A:D.460

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.58, C.61, C.68, H.71 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.58, A:C.61, A:C.68, A:H.71 ZN.3: 4 residues within 4Å: Chain A: C.98, C.101, C.146, C.149 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.98, A:C.101, A:C.146, A:C.149 ZN.4: 3 residues within 4Å: Chain A: R.573, C.580, H.582 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:R.573, A:C.580, A:H.582 ZN.5: 5 residues within 4Å: Chain B: C.1060, C.1063, C.1078, H.1081, S.1085 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1060, B:C.1063, B:C.1078, B:H.1081 ZN.7: 4 residues within 4Å: Chain K: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.7, K:C.10, K:C.44, K:C.45 ZN.8: 5 residues within 4Å: Chain L: C.6, E.12, C.26, Y.28, C.29 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.6, L:E.12, L:E.12, L:C.26, L:C.29

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.6: 11 residues within 4Å: Chain D: C.183, E.185, V.187, F.188, C.203, I.204, C.206, E.207, E.208, C.209, I.219 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.203, D:C.206, D:C.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pilotto, S. et al., Structural basis of RNA polymerase inhibition by viral and host factors. Nat Commun (2021)

Release Date

2021-08-25

Peptides

DNA-directed RNA polymerase subunit A': A
DNA-directed RNA polymerase subunit B: B
DNA-directed RNA polymerase subunit A'': C
DNA-directed RNA polymerase subunit D: D
DNA-directed RNA polymerase subunit E: E
DNA-directed RNA polymerase, subunit F: F
DNA-directed RNA polymerase, subunit G: G
DNA-directed RNA polymerase subunit H: H
DNA-directed RNA polymerase subunit K: I
DNA-directed RNA polymerase subunit L: J
DNA-directed RNA polymerase subunit N: K
DNA-directed RNA polymerase subunit P: L
Conserved protein: M
RNAP inhibitory protein: N

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
K

J
L

K
N

L
P

M
Q

N
Z

DNA-directed RNA polymerase subunit A'

DNA-directed RNA polymerase subunit B

DNA-directed RNA polymerase subunit A''

DNA-directed RNA polymerase subunit D

DNA-directed RNA polymerase subunit E

DNA-directed RNA polymerase, subunit F

DNA-directed RNA polymerase, subunit G

DNA-directed RNA polymerase subunit H

DNA-directed RNA polymerase subunit K

DNA-directed RNA polymerase subunit L

DNA-directed RNA polymerase subunit N

DNA-directed RNA polymerase subunit P

Conserved protein

RNAP inhibitory protein

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