9PHA | pdb_00009pha

CryoEM structure of the YonE portal protein from Bacillus phage SPbeta

• PDB DOI: https://doi.org/10.2210/pdb9PHA/pdb
• EM Map EMD-71643: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Spbetavirus SPbeta
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-09 Released: 2025-12-31 
• Deposition Author(s): Mishra, B.P., Ve, T.
• Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular characterisation of the Bacillus subtilis SpbK antiphage defence system.

Mishra, B.P., Loyo, C.L., Cai, Y., Litfin, T., Miraj, G., Brillault, L., Masic, V., Mosaiab, T., Rajaratnam, P., Rudrawar, S., Gu, W., Kobe, B., Gerdt, J.P., Grossman, A.D., Shi, Y., Ve, T.

(2025) Nat Commun 17: 1051-1051

• PubMed: 41462020 
• DOI: https://doi.org/10.1038/s41467-025-67810-5
• Primary Citation of Related Structures:  
  9PHA, 9PHB


• PubMed Abstract: 
  

  Bacteria have a variety of mechanisms for limiting predation by phages. SpbK is a Toll/interleukin-1 receptor (TIR) domain-containing antiphage defence protein from Bacillus subtilis that provides protection against the temperate phage SPβ via abortive infection. Here we structurally characterise SpbK and its interaction with the SPβ protein YonE. We demonstrate that SpbK is an NADase that produces both ADP-ribose (ADPR) and canonical cyclic ADPR with a N1-glycosidic bond (cADPR, also referred to as N1-cADPR). Combining cryo-EM, in silico predictions, site-directed mutagenesis, and phage infection assays, we show that formation of two-stranded head-to-tail assemblies of SpbK TIR domains is required for both NADase activity and antiphage defence. We also demonstrate that YonE is a dodecameric portal protein that activates the NADase function of SpbK by facilitating TIR domain clustering. Collectively, our results provide insight into how bacterial TIR NADases recognise phage infection.

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Organizational Affiliation: 
• Institute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Chemistry, Indiana University, Bloomington, IN, USA.
Structural Biology Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, Australia.
Centre for Microscopy and Microanalysis, University of Queensland, St Lucia, QLD, Australia.
School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia.
School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, QLD, Australia.
Institute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia. [e-mail].
Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia. [e-mail].
Institute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C12  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 666.34 kDa 
• Atom Count: 30,144 
• Modeled Residue Count: 3,600 
• Deposited Residue Count: 5,820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPbeta prophage-derived uncharacterized protein YonE	A, B, C, D, E, F, G, H, I, J, K, L	485	Spbetavirus SPbeta	Mutation(s): 0  Gene Names: yonE, BSU21120
UniProt
Find proteins for O31953 (Bacillus subtilis (strain 168)) Explore O31953  Go to UniProtKB:  O31953

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Mishra, B.P., Ve, T.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FT200100572
National Health and Medical Research Council (NHMRC, Australia)	Australia	1196590

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release
  
• Version 1.1: 2026-01-14
  Changes: Data collection, Database references
• Version 1.2: 2026-02-04
  Changes: Data collection, Database references