RCSB PDB - 9E4W: Structure of Bacillus phage SPO1 anti-CBASS 4 (Acb4) in complex with 3'3'-cGAMP

 9E4W

Structure of Bacillus phage SPO1 anti-CBASS 4 (Acb4) in complex with 3'3'-cGAMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

Starting Model: in silico
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Ligand Structure Quality Assessment 

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Literature

A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense.

Chang, R.B.Toyoda, H.C.Hobbs, S.J.Richmond-Buccola, D.Wein, T.Burger, N.Chouchani, E.T.Sorek, R.Kranzusch, P.J.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.12.30.630793
  • Primary Citation of Related Structures:  
    9E4W

  • PubMed Abstract: 

    Cyclic oligonucleotide-based antiviral signaling systems (CBASS) are bacterial anti-phage defense operons that use nucleotide signals to control immune activation. Here we biochemically screen 57 diverse E. coli and Bacillus phages for the ability to disrupt CBASS immunity and discover anti-CBASS 4 (Acb4) from the Bacillus phage SPO1 as the founding member of a large family of >1,300 immune evasion proteins. A 2.1 Å crystal structure of Acb4 in complex with 3'3'-cGAMP reveals a tetrameric assembly that functions as a sponge to sequester CBASS signals and inhibit immune activation. We demonstrate Acb4 alone is sufficient to disrupt CBASS activation in vitro and enable immune evasion in vivo . Analyzing phages that infect diverse bacteria, we explain how Acb4 selectively targets nucleotide signals in host defense and avoids disruption of cellular homeostasis. Together, our results reveal principles of immune evasion protein evolution and explain a major mechanism phages use to inhibit host immunity.


  • Organizational Affiliation

    Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-CBASS 4 (Acb4)
A, B, C, D, E
97Bacillus phage SPO1Mutation(s): 0 
UniProt
Find proteins for B6V2Y3 (Bacillus phage SP01)
Explore B6V2Y3 
Go to UniProtKB:  B6V2Y3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6V2Y3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4BW (Subject of Investigation/LOI)
Query on 4BW

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth H]
CA [auth I]
DA [auth J]
EA [auth K]
2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one
C20 H24 N10 O13 P2
RFCBNSCSPXMEBK-INFSMZHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.284α = 87.529
b = 56.496β = 89.02
c = 167.581γ = 81.58
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4BWClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1DP2GM146250-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release