SMTL ID : 6z9r.1

Transcription termination intermediate complex 3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE

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

6 x MG: MAGNESIUM ION

MG.2: 4 residues within 4Å: Chain C: T.185, R.212 Ligands: ADP.1, BEF.3 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.185, H2O.1, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain D: T.185 Ligands: ADP.4, BEF.6 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.185, H2O.1, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain E: K.184, T.185 Ligands: ADP.7, BEF.9 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.185, H2O.1, H2O.1, H2O.1 MG.11: 4 residues within 4Å: Chain F: T.185, R.212 Ligands: ADP.10, BEF.12 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.185, H2O.1, H2O.1, H2O.1 MG.14: 3 residues within 4Å: Chain G: T.185 Ligands: ADP.13, BEF.15 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:T.185, H2O.1, H2O.1, H2O.1 MG.16: 4 residues within 4Å: Chain M: D.460, D.462, D.464 Chain P: C.99 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:D.460, M:D.460, M:D.462, M:D.464

5 x BEF: BERYLLIUM TRIFLUORIDE ION

BEF.3: 8 residues within 4Å: Chain B: R.366 Chain C: P.180, K.184, R.212, R.269, L.320 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.6: 8 residues within 4Å: Chain C: R.366 Chain D: P.180, K.181, K.184, T.185, R.212 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.9: 7 residues within 4Å: Chain D: R.366 Chain E: P.180, K.181, A.182, K.184 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.12: 9 residues within 4Å: Chain E: G.337, R.366 Chain F: K.181, K.184, T.185, R.212, R.269 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 7 residues within 4Å: Chain F: R.366 Chain G: P.180, K.181, K.184, R.212 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION

ZN.17: 5 residues within 4Å: Chain M: C.70, L.71, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.70, M:C.72, M:C.85, M:C.88 ZN.18: 6 residues within 4Å: Chain M: C.814, C.888, D.889, T.890, C.895, C.898 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:C.814, M:C.895

1 x DG: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE

DG.19: 2 residues within 4Å: Chain C: A.74 Chain O: C.36 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Said, N. et al., Snapshots along a factor-mediated, elongation complex-dependent path to transcription termination. To Be Published

Release Date

2020-11-04

Peptides

Transcription termination/antitermination protein NusG: A
Transcription termination factor Rho: BCDEFG
Transcription termination/antitermination protein NusA: H
DNA-directed RNA polymerase subunit alpha: IJ
DNA-directed RNA polymerase subunit omega: K
DNA-directed RNA polymerase subunit beta: L
DNA-directed RNA polymerase subunit beta': M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
f

C
a

D
b

E
c

F
d

G
e

H
A

I
U

J
V

K
W

L
X

M
Y

Transcription termination/antitermination protein NusG

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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