SMTL ID : 8e5p.1

Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.1: 12 residues within 4Å: Chain B: P.179, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain C: R.366, K.367 Ligands: MG.2, BEF.3 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:K.181, B:A.182, B:G.183, B:K.184, B:T.185, B:T.185, B:M.186, C:K.367 Salt bridges: B:K.184, B:K.184, C:R.366, C:R.366 pi-Stacking: B:F.355, B:F.355 pi-Cation interactions: C:K.367 ADP.4: 12 residues within 4Å: Chain C: P.179, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain F: R.366, K.367 Ligands: MG.5, BEF.6 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:K.181, C:A.182, C:G.183, C:K.184, C:T.185, C:T.185, C:T.185, C:M.186, F:K.367 Salt bridges: C:K.184, C:K.184, F:R.366, F:R.366 pi-Stacking: C:F.355, C:F.355 ADP.7: 12 residues within 4Å: Chain D: P.179, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain G: R.366, K.367 Ligands: MG.8, BEF.9 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain G Hydrogen bonds: D:K.181, D:A.182, D:G.183, D:K.184, D:K.184, D:T.185, D:T.185, D:M.186, G:K.367 Salt bridges: D:K.184, D:K.184, G:R.366, G:R.366 pi-Stacking: D:F.355, D:F.355 ADP.10: 12 residues within 4Å: Chain D: R.366, K.367 Chain E: P.179, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.11, BEF.12 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:K.181, E:A.182, E:G.183, E:K.184, E:T.185, E:T.185, E:T.185, E:M.186, D:K.367 Salt bridges: E:K.184, E:K.184, D:R.366, D:R.366 pi-Stacking: E:F.355, E:F.355 ADP.13: 12 residues within 4Å: Chain E: R.366, K.367 Chain F: P.179, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.14, BEF.15 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:K.181, F:A.182, F:G.183, F:K.184, F:T.185, F:T.185, F:T.185, F:M.186, E:K.367 Salt bridges: F:K.184, F:K.184, E:R.366, E:R.366 pi-Stacking: F:F.355, F:F.355 ADP.16: 12 residues within 4Å: Chain B: R.366, K.367 Chain G: P.179, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.17, BEF.18 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain B Hydrogen bonds: G:K.181, G:A.182, G:G.183, G:K.184, G:K.184, G:T.185, G:M.186, B:K.367 Salt bridges: G:K.184, G:K.184, B:R.366, B:R.366 pi-Stacking: G:F.355, G:F.355

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: K.184, T.185 Ligands: ADP.1, BEF.3 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain C: K.184, T.185 Ligands: ADP.4, BEF.6 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain D: K.184, T.185 Ligands: ADP.7, BEF.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain E: K.184, T.185 Ligands: ADP.10, BEF.12 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain F: K.184, T.185 Ligands: ADP.13, BEF.15 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain G: K.184, T.185 Ligands: ADP.16, BEF.18 No protein-ligand interaction detected (PLIP)

6 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.3: 8 residues within 4Å: Chain B: P.180, K.181, K.184, L.320 Chain C: G.337, R.366 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.6: 8 residues within 4Å: Chain C: P.180, K.181, K.184, L.320 Chain F: G.337, R.366 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.9: 8 residues within 4Å: Chain D: P.180, K.181, K.184, L.320 Chain G: G.337, R.366 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.12: 8 residues within 4Å: Chain D: G.337, R.366 Chain E: P.180, K.181, K.184, L.320 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 8 residues within 4Å: Chain E: G.337, R.366 Chain F: P.180, K.181, K.184, L.320 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) BEF.18: 8 residues within 4Å: Chain B: G.337, R.366 Chain G: P.180, K.181, K.184, L.320 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Molodtsov, V. et al., Structural basis of Rho-dependent transcription termination. Nature (2023)

Release Date

2022-09-07

Peptides

Transcription termination factor Rho: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
e

C
f

D
c

E
b

F
a

G
d

Transcription termination factor Rho

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