9FF7 | pdb_00009ff7

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Nucleotide-induced hyper-oligomerization inactivates transcription termination factor rho.

Wang, B.Said, N.Hilal, T.Finazzo, M.Wahl, M.C.Artsimovitch, I.

(2025) Nat Commun 16: 1653-1653

  • DOI: https://doi.org/10.1038/s41467-025-56824-8
  • Primary Citation of Related Structures:  
    9FF7

  • PubMed Abstract: 

    Bacterial RNA helicase ρ is a genome sentinel that terminates the synthesis of damaged and junk RNAs that are not translated by the ribosome. It is unclear how ρ is regulated during dormancy or stress, when translation is inefficient and RNAs are vulnerable to ρ-mediated release. We use cryogenic electron microscopy, biochemical, and genetic approaches to show that substitutions of residues in the connector between two ρ domains or ADP promote the formation of extended Escherichia coli ρ filaments. By contrast, (p)ppGpp induces the formation of transient ρ dodecamers. Our results demonstrate that ADP and (p)ppGpp nucleotides bound at subunit interfaces inhibit ρ ring closure that underpins the hexamer activation, thus favoring the assembly of inactive higher-order oligomers. Connector substitutions and antibiotics that inhibit RNA and protein syntheses trigger ρ aggregation in the cell. These and other recent data implicate aggregation as a widespread strategy to tune ρ activity.


  • Organizational Affiliation
    • Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor Rho
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
418Escherichia coliMutation(s): 2 
Gene Names: rhoZ5293ECs4716
EC: 3.6.4
UniProt
Find proteins for P0AG30 (Escherichia coli (strain K12))
Explore P0AG30 
Go to UniProtKB:  P0AG30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG30
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ME7
Query on ME7

Download Ideal Coordinates CCD File 
M [auth B],
O [auth C],
Q [auth D],
R [auth E],
U [auth L]
1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)
C10 H8 N2 O4
PUKLCKVOVCZYKF-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth C],
P [auth D],
S [auth I],
T [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459:
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany433623608

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release