SMTL ID : 7add.1

Transcription termination intermediate complex IIIa

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-2-1-1-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: R.366, K.367, E.369 Chain B: P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Ligands: MG.2, BEF.3 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.181, B:A.182, B:G.183, B:K.184, B:T.185, B:T.185, B:R.212, A:K.367, A:E.369 Water bridges: B:K.184, B:T.185, B:T.185, B:R.212 Salt bridges: B:K.184 pi-Stacking: B:F.355, B:F.355 ADP.4: 12 residues within 4Å: Chain B: R.366, K.367, E.369 Chain C: T.158, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.5, BEF.6 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:T.158, C:T.158, C:A.182, C:K.184, C:T.185, C:T.185, C:M.186, B:K.367, B:K.367, B:E.369 Salt bridges: C:K.184, B:K.367 pi-Stacking: C:F.355, C:F.355 ADP.7: 13 residues within 4Å: Chain C: R.366, K.367, E.369 Chain D: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.8, BEF.9 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.158, D:K.181, D:A.182, D:K.184, D:T.185, D:M.186, C:K.367, C:K.367, C:E.369 Water bridges: D:R.212, D:E.215 Salt bridges: D:K.184 pi-Stacking: D:F.355, D:F.355 ADP.11: 12 residues within 4Å: Chain D: R.366, E.369 Chain E: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: BEF.10, MG.12 14 PLIP interactions: 4 interactions with chain D, 10 interactions with chain E Hydrogen bonds: D:R.366, D:K.367, D:E.369, E:T.158, E:K.181, E:A.182, E:K.184, E:T.185 Salt bridges: D:K.367, E:K.184 Water bridges: E:T.185, E:T.185, E:R.212 pi-Stacking: E:F.355 ADP.13: 14 residues within 4Å: Chain E: R.366, K.367, E.369 Chain F: T.158, P.180, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.14, BEF.15 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:T.158, F:A.182, F:G.183, F:K.184, F:T.185, E:K.367, E:K.367, E:E.369 Water bridges: F:K.184, F:K.184, F:T.185, F:R.212, F:R.212, F:E.215 Salt bridges: F:K.184 pi-Stacking: F:F.355, F: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 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.185, H2O.1, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain C: K.184, T.185 Ligands: ADP.4, BEF.6 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.185, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain D: K.184, T.185 Ligands: ADP.7, BEF.9 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.185, H2O.1, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain E: K.184, T.185 Ligands: BEF.10, ADP.11 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.185, H2O.1 MG.14: 4 residues within 4Å: Chain F: K.184, T.185 Ligands: ADP.13, BEF.15 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.185, H2O.1, H2O.1 MG.16: 4 residues within 4Å: Chain L: D.460, D.462, D.464 Chain O: C.99 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:D.460, L:D.460, L:D.462, L:D.462, L:D.464

5 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 7 residues within 4Å: Chain A: R.366 Chain B: K.184, R.212, R.269, L.320 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.6: 7 residues within 4Å: Chain B: R.366 Chain C: P.180, K.181, K.184, R.212 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.9: 7 residues within 4Å: Chain C: R.366 Chain D: P.180, K.184, T.185, R.212 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.10: 7 residues within 4Å: Chain D: R.366 Chain E: P.180, K.181, K.184, R.212 Ligands: ADP.11, MG.12 No protein-ligand interaction detected (PLIP) BEF.15: 8 residues within 4Å: Chain E: R.366 Chain F: P.180, K.181, K.184, R.212, R.269 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.17: 5 residues within 4Å: Chain L: C.70, L.71, C.72, C.85, V.90 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.70, L:C.72, L:C.85 ZN.18: 5 residues within 4Å: Chain L: C.814, C.888, D.889, C.895, C.898 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.814, L:C.888, L:C.895, L:C.898

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Said, N. et al., Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho. Science (2021)

Release Date

2020-11-25

Peptides

Transcription termination factor Rho: ABCDEF
Transcription termination/antitermination protein NusA: G
DNA-directed RNA polymerase subunit alpha: HI
DNA-directed RNA polymerase subunit omega: J
DNA-directed RNA polymerase subunit beta: K
DNA-directed RNA polymerase subunit beta': L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
f

B
a

C
b

D
c

E
d

F
e

G
A

H
U

I
V

J
W

K
X

L
Y

Transcription termination factor Rho

Transcription termination/antitermination protein NusA

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit omega

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

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