SMTL ID : 9ff7.1

Structure of the BMOE-crosslinked transcription termination factor Rho in the presence of ppGpp; S84C/M405C double mutant

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

5 x ME7: 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)(Non-covalent)

ME7.1: 4 residues within 4Å: Chain B: C.84, R.87 Chain K: S.82, C.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.87, B:R.87 ME7.3: 6 residues within 4Å: Chain C: P.83, C.84, R.87 Chain J: S.82, P.83, C.84 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain C Hydrophobic interactions: J:P.83, C:R.87 Hydrogen bonds: J:S.82 pi-Cation interactions: C:R.87 ME7.5: 5 residues within 4Å: Chain D: S.82, C.84 Chain I: S.82, P.83, C.84 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:C.84 ME7.6: 2 residues within 4Å: Chain E: C.84 Chain H: C.84 No protein-ligand interaction detected (PLIP) ME7.9: 4 residues within 4Å: Chain A: S.82, C.84 Chain L: C.84, R.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.82

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain C: S.346, R.347, K.348, I.349, A.350 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.346, C:R.347 MG.4: 4 residues within 4Å: Chain D: H.344, L.345, S.346, D.359 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.344, D:L.345 MG.7: 4 residues within 4Å: Chain I: P.179, P.180, K.181, A.182 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:P.179, I:P.180 MG.8: 6 residues within 4Å: Chain J: H.344, L.345, S.346, A.357, I.358, D.359 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:H.344, J:A.357

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Nucleotide-induced hyper-oligomerization inactivates transcription termination factor rho. Nat Commun (2025)

Release Date

2025-04-09

Peptides

Transcription termination factor Rho: ABCDEFGHIJKL

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

L
L

Transcription termination factor Rho