8PTM

Structure of the transcription termination factor Rho in complex with Rof and ADP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Sm-like protein Rof inhibits transcription termination factor rho by binding site obstruction and conformational insulation.

Said, N.Finazzo, M.Hilal, T.Wang, B.Selinger, T.L.Gjorgjevikj, D.Artsimovitch, I.Wahl, M.C.

(2024) Nat Commun 15: 3186-3186

  • DOI: https://doi.org/10.1038/s41467-024-47439-6
  • Primary Citation of Related Structures:  
    8PTG, 8PTM, 8PTN, 8PTO, 8PTP

  • PubMed Abstract: 

    Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits ρ-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Here, our cryo-EM structures of ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirms that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses reveal that Rof is restricted to Pseudomonadota and that the ρ-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ may be detrimental.


  • Organizational Affiliation

    Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor Rho
A, B, C, D, E
A, B, C, D, E, F
419Escherichia coliMutation(s): 0 
Gene Names: rhonitApsuArnsCsbaAtsub3783JW3756
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein rofG [auth a],
H [auth b],
I [auth c],
J [auth d],
K [auth e]
86Escherichia coliMutation(s): 0 
Gene Names: rofyaeOb0189JW0184
UniProt
Find proteins for P0AFW8 (Escherichia coli (strain K12))
Explore P0AFW8 
Go to UniProtKB:  P0AFW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFW8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.20_4459:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany392923329
German Research Foundation (DFG)Germany433623608

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Database references