9PHA

CryoEM structure of the YonE portal protein from Bacillus phage SPbeta

Summary for 9PHA

• Entry DOI: 10.2210/pdb9pha/pdb
• EMDB information: 71643
• Descriptor: SPbeta prophage-derived uncharacterized protein YonE (1 entity in total)
• Functional Keywords: portal protein, antiphage defence, viral protein
• Biological source: Spbetavirus SPbeta
• Total number of polymer chains: 12
• Total formula weight: 666340.69

Authors

Mishra, B.P.,Ve, T. (deposition date: 2025-07-09, release date: 2025-12-31, Last modification date: 2026-01-14)

Primary citation

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.
Molecular characterisation of the Bacillus subtilis SpbK antiphage defence system.
Nat Commun, 2025

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.

PubMed: 41462020
DOI: 10.1038/s41467-025-67810-5

Experimental method

ELECTRON MICROSCOPY (3.3 Å)