SMTL ID : 8ptg.1

Structure of the transcription termination factor Rho bound to RNA at the PBS and SBS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.212, E.215, F.355 Chain B: R.366, K.367 Ligands: MG.2, BEF.3 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.158, A:K.181, A:A.182, A:G.183, A:K.184, A:T.185, A:T.185, A:M.186, A:R.212, B:K.367 Salt bridges: A:K.184, B:R.366, B:R.366 pi-Stacking: A:F.355, A:F.355 ADP.4: 15 residues within 4Å: Chain B: T.158, P.179, P.180, K.181, A.182, G.183, K.184, T.185, M.186, E.215, F.355 Chain C: R.366, K.367 Ligands: MG.5, BEF.6 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:T.158, 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, C:R.366, C:R.366 pi-Stacking: B:F.355, B:F.355 ADP.7: 14 residues within 4Å: Chain C: T.158, P.180, K.181, A.182, G.183, K.184, T.185, M.186, E.215, F.355 Chain D: R.366, K.367 Ligands: MG.8, BEF.9 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.158, C:K.181, C:A.182, C:G.183, C:K.184, C:T.185, C:T.185, C:M.186, D:K.367 Salt bridges: C:K.184, D:R.366, D:R.366 pi-Stacking: C:F.355, C:F.355 ADP.10: 15 residues within 4Å: Chain D: T.158, P.180, K.181, A.182, G.183, K.184, T.185, M.186, E.215, F.355 Chain E: T.365, R.366, K.367 Ligands: MG.11, BEF.12 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:T.158, D:T.158, D:K.181, D:A.182, D:G.183, D:K.184, D:T.185, D:M.186, E:T.365, E:K.367 Salt bridges: D:K.184, E:R.366, E:R.366 pi-Stacking: D:F.355, D:F.355 ADP.13: 13 residues within 4Å: Chain E: P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain F: R.366, K.367 Ligands: MG.14, BEF.15 13 PLIP interactions: 3 interactions with chain F, 10 interactions with chain E Hydrogen bonds: F:R.366, F:K.367, E:K.181, E:A.182, E:G.183, E:K.184, E:T.185, E:M.186, E:R.212 Salt bridges: F:R.366, E:K.184 pi-Stacking: E:F.355, E:F.355 ADP.16: 13 residues within 4Å: Chain A: R.366, K.367 Chain F: P.180, K.181, A.182, G.183, K.184, T.185, M.186, E.215, F.355 Ligands: MG.17, BEF.18 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:K.181, F:A.182, F:G.183, F:K.184, F:T.185, F:T.185, F:M.186, A:K.367 Salt bridges: F:K.184, A:R.366, A:R.366 pi-Stacking: F:F.355, F:F.355

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.185, E.211, R.212, E.215 Ligands: ADP.1, BEF.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.185 MG.5: 6 residues within 4Å: Chain B: T.185, E.211, R.212, E.215 Ligands: ADP.4, BEF.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.185 MG.8: 7 residues within 4Å: Chain C: T.185, E.211, R.212, E.215, D.265 Ligands: ADP.7, BEF.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.185 MG.11: 5 residues within 4Å: Chain D: T.185, R.212, E.215 Ligands: ADP.10, BEF.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.185 MG.14: 4 residues within 4Å: Chain E: T.185, E.211 Ligands: ADP.13, BEF.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.185 MG.17: 5 residues within 4Å: Chain F: T.185, E.211, D.265 Ligands: ADP.16, BEF.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.185

6 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)(Covalent)

BEF.3: 8 residues within 4Å: Chain A: P.179, P.180, K.181, K.184, L.320 Chain B: R.366 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.6: 9 residues within 4Å: Chain B: P.180, K.181, K.184, R.212 Chain C: K.336, G.337, R.366 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.9: 10 residues within 4Å: Chain C: P.179, P.180, K.181, K.184, R.212, L.320 Chain D: G.337, R.366 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.12: 10 residues within 4Å: Chain D: P.179, P.180, K.181, K.184, R.212, L.320 Chain E: K.336, R.366 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 8 residues within 4Å: Chain E: P.179, P.180, K.181, A.182, K.184 Chain F: R.366 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) BEF.18: 9 residues within 4Å: Chain A: R.366 Chain F: P.179, P.180, K.181, K.184, R.212, L.320 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Said, N. et al., Sm-like protein Rof inhibits transcription termination factor rho by binding site obstruction and conformational insulation. Nat Commun (2024)

Release Date

2024-04-17

Peptides

Transcription termination factor Rho: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Transcription termination factor Rho

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