SMTL ID : 8hsr.1

Thermus thermophilus Rho-engaged RNAP elongation complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: K.189, A.190, G.191, K.192, T.193, T.194, L.195, E.223, F.364 Chain B: R.375 Ligands: MG.2, BEF.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.189, A:A.190, A:G.191, A:T.193, A:T.194, A:T.194, B:R.375, B:R.376 Salt bridges: A:K.192, B:R.375 pi-Stacking: A:F.364, A:F.364 ADP.4: 17 residues within 4Å: Chain B: P.187, P.188, K.189, A.190, G.191, K.192, T.193, T.194, L.195, K.198, E.219, E.223, L.329, F.364 Chain C: R.375 Ligands: BEF.5, MG.6 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:A.190, B:G.191, B:K.192, B:T.193, B:T.193, B:T.194, B:T.194, B:L.195, B:K.198, B:K.198, B:E.223, C:R.375 Salt bridges: B:K.192, C:R.375, C:R.375 pi-Stacking: B:F.364 ADP.7: 16 residues within 4Å: Chain C: P.188, K.189, A.190, G.191, K.192, T.193, T.194, L.195, K.198, E.219, R.220, E.223, F.364 Chain D: R.375 Ligands: MG.8, BEF.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.189, C:A.190, C:G.191, C:K.192, C:T.193, C:T.193, C:T.194, C:K.198 Salt bridges: C:K.192, C:K.192, C:R.220 pi-Stacking: C:F.364 ADP.10: 17 residues within 4Å: Chain D: P.187, P.188, K.189, A.190, G.191, K.192, T.193, T.194, L.195, K.198, E.219, R.220, L.329, F.364 Chain E: R.375 Ligands: MG.11, BEF.12 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:K.189, D:A.190, D:G.191, D:K.192, D:T.193, D:K.198, D:K.198, D:R.220, E:R.375, E:R.375 Salt bridges: D:K.192, D:K.192 ADP.13: 13 residues within 4Å: Chain E: P.187, P.188, K.189, A.190, G.191, K.192, T.193, T.194, L.195, K.198, F.364 Ligands: MG.14, BEF.15 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:A.190, E:G.191, E:K.192, E:T.193, E:T.193, E:K.198, E:K.198 Salt bridges: E:K.192, E:K.192 ADP.16: 15 residues within 4Å: Chain A: R.375, R.376 Chain F: P.187, P.188, K.189, A.190, G.191, K.192, T.193, T.194, E.219, E.359, F.364 Ligands: MG.17, BEF.18 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:A.190, F:G.191, F:K.192, F:T.193, F:T.193, F:T.193, F:T.194, F:T.194, F:E.359, A:R.376, A:R.376 Salt bridges: F:K.192

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.193, E.219, E.223 Ligands: ADP.1, BEF.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.193 MG.6: 6 residues within 4Å: Chain B: T.193, R.220, E.223 Chain C: R.375 Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP) MG.8: 7 residues within 4Å: Chain C: T.193, E.219, R.220, E.223, D.274 Ligands: ADP.7, BEF.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.193, C:E.219 MG.11: 4 residues within 4Å: Chain D: T.193, E.219 Ligands: ADP.10, BEF.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.193 MG.14: 4 residues within 4Å: Chain E: T.193, R.220 Ligands: ADP.13, BEF.15 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain F: T.193, E.219 Ligands: ADP.16, BEF.18 No protein-ligand interaction detected (PLIP) MG.21: 5 residues within 4Å: Chain J: D.739, D.741, D.743 Chain M: C.124, U.125 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.739, J:D.741, J:D.741, J:D.743

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

BEF.3: 7 residues within 4Å: Chain A: P.188, K.189, A.190, G.191, K.192 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.5: 10 residues within 4Å: Chain B: T.193, E.219, R.220, E.223, D.274, R.278 Chain C: G.346, R.375 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) BEF.9: 9 residues within 4Å: Chain C: E.219, R.220, E.223, D.274, S.275, R.278 Chain D: G.346 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.12: 9 residues within 4Å: Chain D: P.188, K.189, E.219, R.220, R.278 Chain E: G.346, R.375 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 10 residues within 4Å: Chain E: K.189, K.192, E.219, R.220, R.278, L.329 Chain F: G.346, R.375 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) BEF.18: 11 residues within 4Å: Chain A: G.346, R.375 Chain F: P.188, K.189, E.219, R.220, S.275, R.278, L.329 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.19: 5 residues within 4Å: Chain J: C.58, C.60, G.61, C.73, C.76 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.58, J:C.60, J:C.73, J:C.76 ZN.20: 5 residues within 4Å: Chain J: C.1112, T.1114, C.1194, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.1112, J:C.1194, J:C.1201, J:C.1204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murayama, Y. et al., Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. Sci Adv (2023)

Release Date

2023-05-03

Peptides

Transcription termination factor Rho: ABCDEF
DNA-directed RNA polymerase subunit alpha: GH
DNA-directed RNA polymerase subunit beta: I
DNA-directed RNA polymerase subunit beta': J
DNA-directed RNA polymerase subunit omega: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

Transcription termination factor Rho

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

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