8RSU

Rap from bacteriophage Phi3T in presence of pheromone RRGHTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Extracellular proteolysis of tandemly duplicated pheromone propeptides affords additional complexity to bacterial quorum sensing.

Felipe-Ruiz, A.Zamora-Caballero, S.Bendori, S.O.Penades, J.R.Eldar, A.Marina, A.

(2024) PLoS Biol 22: e3002744-e3002744

  • DOI: https://doi.org/10.1371/journal.pbio.3002744
  • Primary Citation of Related Structures:  
    8RST, 8RSU, 8RSV, 8RTC, 8RTE

  • PubMed Abstract: 

    Bacterial interactions are vital for adapting to changing environments, with quorum sensing (QS) systems playing a central role in coordinating behaviors through small signaling molecules. The RRNPPA family is the prevalent QS systems in Bacillota and mediating communication through secreted oligopeptides, which are processed into active pheromones by extracellular proteases. Notably, in several cases the propeptides show the presence of multiple putative pheromones within their sequences, which has been proposed as a mechanism to diversify peptide-receptor specificity and potentially facilitate new functions. However, neither the processes governing the maturation of propeptides containing multiple pheromones, nor their functional significance has been evaluated. Here, using 2 Rap systems from bacteriophages infecting Bacillus subtilis that exhibit different types of pheromone duplication in their propeptides, we investigate the maturation process and the molecular and functional activities of the produced pheromones. Our results reveal that distinct maturation processes generate multiple mature pheromones, which bind to receptors with varying affinities but produce identical structural and biological responses. These findings add additional layers in the complexity of QS communication and regulation, opening new possibilities for microbial social behaviors, highlighting the intricate nature of bacterial interactions and adaptation.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rap3T379Bacillus phage phi3TMutation(s): 0 
Gene Names: phi3T_14
UniProt
Find proteins for A0A1P8CWN8 (Bacillus phage phi3T)
Explore A0A1P8CWN8 
Go to UniProtKB:  A0A1P8CWN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1P8CWN8
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pheromone RRGHTA6Bacillus phage phi3TMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H22
Query on A1H22

Download Ideal Coordinates CCD File 
C [auth A]Glycerol ethoxylate
C39 H80 O21
PVDRPYVNUSQYRG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.07α = 90
b = 194.031β = 90
c = 93.534γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2022-137201NB-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainFPU19/00433

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Database references