9FKU | pdb_00009fku

Crystal Structure of AimR from Katmira phage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.212 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Phages communicate across species to shape microbial ecosystems.

Gallego-Del-Sol, F.Sin, D.Chmielowska, C.Mancheno-Bonillo, J.Li, Y.Zamora-Caballero, S.Quiles-Puchalt, N.Penades, J.R.Marina, A.

(2026) Cell 189: 3025-3038.e12

  • DOI: https://doi.org/10.1016/j.cell.2026.03.004
  • Primary Citation Related Structures: 
    9F36, 9F82, 9F9R, 9FKU

  • PubMed Abstract: 

    Arbitrium is a communication system that helps bacteriophages to decide between lysis and lysogeny through secreted peptides. In this system, the arbitrium communication peptide (AimP) binds its cognate arbitrium receptor (AimR) to repress aimX (a negative regulator of lysogeny) expression, promoting lysogeny. It has been assumed that each AimR responds exclusively to its own AimP. Here, we challenge this view by demonstrating cross-communication between arbitrium systems. Using prototypical arbitrium phages, we show that AimP peptides can bind and repress non-cognate AimR receptors, promoting lysogeny and reducing prophage induction. Structural and biochemical analyses reveal conserved receptor features that permit cross-recognition of non-cognate peptides while preserving recognition of cognate partners. In mixed lysogenic cultures, these interactions alter induction outcomes, underscoring their ecological significance. Extending to infection contexts, we demonstrate that crosstalk favors lysogeny of incoming phages in cells harboring compatible systems. These findings establish that phages engage in cross-species communication via peptide signaling, reshaping microbial communities in unexpected ways.


  • Organizational Affiliation
    • Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, 46010 Valencia, Spain.

Macromolecule Content 

  • Total Structure Weight: 92.17 kDa 
  • Atom Count: 6,875 
  • Modeled Residue Count: 784 
  • Deposited Residue Count: 784 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arbitrium receptor
A, B
386Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for O31927 (Bacillus subtilis (strain 168))
Explore O31927 
Go to UniProtKB:  O31927
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31927
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GLY-VAL-VAL-ARG-GLY-ALA
C, D
6Bacillus subtilisMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.212 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.765α = 90
b = 203.582β = 90
c = 143.069γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)Spain--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2026-05-27
    Changes: Database references