Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 90.34 kDa 
• Atom Count: 6635 
• Modelled Residue Count: 764 
• Deposited Residue Count: 764 
• Unique protein chains: 1

5ZVV

Structure of SeMet-phAimR

• PDB DOI: 10.2210/pdb5ZVV/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Bacillus phage phi3T
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-05-13 Released: 2018-09-05 
• Deposition Author(s): Cheng, W., Dou, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Structural and functional insights into the regulation of the lysis-lysogeny decision in viral communities.

Dou, C., Xiong, J., Gu, Y., Yin, K., Wang, J., Hu, Y., Zhou, D., Fu, X., Qi, S., Zhu, X., Yao, S., Xu, H., Nie, C., Liang, Z., Yang, S., Wei, Y., Cheng, W.

(2018) Nat Microbiol 3: 1285-1294

• PubMed: 30323253 
• DOI: 10.1038/s41564-018-0259-7
• Primary Citation of Related Structures:  
  5ZVV, 5ZVW, 5ZW5, 5ZW6


• PubMed Abstract: 
  

Communication is vital for all organisms including microorganisms, which is clearly demonstrated by the bacterial quorum-sensing system. However, the molecular mechanisms underlying communication among viruses (phages) via the quorum-sensing-like 'arbitrium' system remain unclear. Viral or host densities are known to be related to an increased prevalence of lysogeny; however, how the switch from the lytic to the lysogenic pathway occurs is unknown. Thus, we sought to reveal mechanisms of communication among viruses and determine the lysogenic dynamics involved. Structural and functional analyses of the phage-derived SAIRGA and GMPRGA peptides and their corresponding receptors, phAimR and spAimR, indicated that SAIRGA directs the lysis-lysogeny decision of phi3T by modulating conformational changes in phAimR, whereas GMPRGA regulates the lysis-lysogeny pathway by stabilizing spAimR in the dimeric state. Although temperate viruses are thought to share a similar lytic-lysogenic cycle switch model, our study suggests the existence of alternative strain-specific mechanisms that regulate the lysis-lysogeny decision. Collectively, these findings provide insights into the molecular mechanisms underlying communication among viruses, offering theoretical applications for the treatment of infectious viral diseases.

---

Organizational Affiliation: 

Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AimR transcriptional regulator	A, B	382	Bacillus phage phi3T	Mutation(s): 0  Gene Names: aimR, phi3T_89
UniProt
Find proteins for P0DOE3 (Bacillus phage phi3T) Explore P0DOE3  Go to UniProtKB:  P0DOE3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.469	α = 90
b = 116.917	β = 113.55
c = 68.244	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHENIX	phasing
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-05-13 
• Released Date: 2018-09-05 
Deposition Author(s): Cheng, W., Dou, C.

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2019-03-13
  Changes: Data collection, Database references, Structure summary