SMTL ID : 8t0l.1

E. coli Sw2/Snf2 ATPase RapA bound to both ADP-AlF3 and reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain D: D.445, D.447, D.449 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.445, D:D.445, D:D.447, D:D.449

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain D: C.55, C.57, C.70, C.73, V.75 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.55, D:C.57, D:C.70, D:C.73 ZN.3: 5 residues within 4Å: Chain D: C.799, R.868, C.873, C.880, C.883 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.799, D:C.873, D:C.880, D:C.883

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

ADP.4: 19 residues within 4Å: Chain F: T.151, S.152, I.154, Q.157, V.178, G.179, L.180, G.181, K.182, T.183, I.184, Q.213, E.217, R.221, N.570, Q.572, R.598, I.599 Ligands: AF3.5 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.152, F:Q.157, F:Q.157, F:G.179, F:G.179, F:G.181, F:K.182, F:T.183, F:T.183, F:Q.213, F:E.217, F:R.221, F:R.221 Salt bridges: F:K.182, F:R.598, F:R.598

1 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.5: 6 residues within 4Å: Chain F: V.178, K.182, T.183, E.280, R.598 Ligands: ADP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brewer, J.J. et al., RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-04-02

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase-associated protein RapA: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
F

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase-associated protein RapA

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