Crystal structure of AimR from Bacillus phage SPbeta

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structural basis of the arbitrium peptide-AimR communication system in the phage lysis-lysogeny decision.

Wang, Q.Guan, Z.Pei, K.Wang, J.Liu, Z.Yin, P.Peng, D.Zou, T.

(2018) Nat Microbiol 3: 1266-1273

  • DOI: https://doi.org/10.1038/s41564-018-0239-y
  • Primary Citation of Related Structures:  
    5XYB, 5Y24

  • PubMed Abstract: 

    A bacteriophage can replicate and release virions from a host cell in the lytic cycle or switch to a lysogenic process in which the phage integrates itself into the host genome as a prophage. In Bacillus cells, some types of phages employ the arbitrium communication system, which contains an arbitrium hexapeptide, the cellular receptor AimR and the lysogenic negative regulator AimX. This system controls the decision between the lytic and lysogenic cycles. However, both the mechanism of molecular recognition between the arbitrium peptide and AimR and how downstream gene expression is regulated remain unknown. Here, we report crystal structures for AimR from the SPbeta phage in the apo form and the arbitrium peptide-bound form at 2.20 Å and 1.92 Å, respectively. With or without the peptide, AimR dimerizes through the C-terminal capping helix. AimR assembles a superhelical fold and accommodates the peptide encircled by its tetratricopeptide repeats, which is reminiscent of RRNPP family members from the quorum-sensing system. In the absence of the arbitrium peptide, AimR targets the upstream sequence of the aimX gene; its DNA binding activity is prevented following peptide binding. In summary, our findings provide a structural basis for peptide recognition in the phage lysis-lysogeny decision communication system.

  • Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AimR transcriptional regulator
A, B
396Spbetavirus SPbetaMutation(s): 0 
Gene Names: aimRyopK
Find proteins for O64094 (Bacillus phage SPbeta)
Explore O64094 
Go to UniProtKB:  O64094
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO64094
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.571α = 90
b = 114.814β = 90
c = 220.444γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.3: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.4: 2024-03-27
    Changes: Data collection, Database references