8PEX | pdb_00008pex

Rho P167L-ATPgS-Psu complex II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Psu protein of phage satellite P4 inhibits transcription termination factor rho by forced hyper-oligomerization.

Gjorgjevikj, D.Kumar, N.Wang, B.Hilal, T.Said, N.Loll, B.Artsimovitch, I.Sen, R.Wahl, M.C.

(2025) Nat Commun 16: 550-550

  • DOI: https://doi.org/10.1038/s41467-025-55897-9
  • Primary Citation of Related Structures:  
    8PEU, 8PEW, 8PEX, 8PEY, 9GCS, 9GCT, 9GCU

  • PubMed Abstract: 

    Many bacteriophages modulate host transcription to favor expression of their own genomes. Phage satellite P4 polarity suppression protein, Psu, a building block of the viral capsid, inhibits hexameric transcription termination factor, ρ, by presently unknown mechanisms. Our cryogenic electron microscopy structures of ρ-Psu complexes show that Psu dimers clamp two inactive, open ρ rings and promote their expansion to higher-oligomeric states. ATPase, nucleotide binding and nucleic acid binding studies revealed that Psu hinders ρ ring closure and traps nucleotides in their binding pockets on ρ. Structure-guided mutagenesis in combination with growth, pull-down, and termination assays further delineated the functional ρ-Psu interfaces in vivo. Bioinformatic analyses revealed that Psu is associated with a wide variety of phage defense systems across Enterobacteriaceae, suggesting that Psu may regulate expression of anti-phage genes. Our findings show that modulation of the ρ oligomeric state via diverse strategies is a pervasive gene regulatory principle in bacteria.


  • Organizational Affiliation

    Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor Rho419Escherichia coliMutation(s): 1 
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
Polarity suppression protein190Enterobacteria phage P4Mutation(s): 0 
Gene Names: psu
UniProt
Find proteins for P05460 (Enterobacteria phage P4)
Explore P05460 
Go to UniProtKB:  P05460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05460
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
AA [auth C]
CA [auth D]
EA [auth E]
GA [auth F]
IA [auth I]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth C]
DA [auth D]
FA [auth E]
HA [auth F]
JA [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459
RECONSTRUCTIONcryoSPARCv3.3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRTG 2473-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references, Structure summary