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- PDB-9pha: CryoEM structure of the YonE portal protein from Bacillus phage SPbeta -

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Basic information

Entry
Database: PDB / ID: 9pha
TitleCryoEM structure of the YonE portal protein from Bacillus phage SPbeta
ComponentsSPbeta prophage-derived uncharacterized protein YonE
KeywordsVIRAL PROTEIN / Portal protein / antiphage defence
Function / homologySPbeta prophage-derived uncharacterized protein YonE
Function and homology information
Biological speciesSpbetavirus SPbeta
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMishra, B.P. / Ve, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT200100572 Australia
National Health and Medical Research Council (NHMRC, Australia)1196590 Australia
CitationJournal: Nat Commun / Year: 2025
Title: Molecular characterisation of the Bacillus subtilis SpbK antiphage defence system.
Authors: Biswa P Mishra / Christian L Loyo / Yanyao Cai / Thomas Litfin / Gause Miraj / Lou Brillault / Veronika Masic / Tamim Mosaiab / Premraj Rajaratnam / Santosh Rudrawar / Weixi Gu / Bostjan ...Authors: Biswa P Mishra / Christian L Loyo / Yanyao Cai / Thomas Litfin / Gause Miraj / Lou Brillault / Veronika Masic / Tamim Mosaiab / Premraj Rajaratnam / Santosh Rudrawar / Weixi Gu / Bostjan Kobe / Joseph P Gerdt / Alan D Grossman / Yun Shi / Thomas Ve /
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 ...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.
History
DepositionJul 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPbeta prophage-derived uncharacterized protein YonE
B: SPbeta prophage-derived uncharacterized protein YonE
C: SPbeta prophage-derived uncharacterized protein YonE
D: SPbeta prophage-derived uncharacterized protein YonE
E: SPbeta prophage-derived uncharacterized protein YonE
F: SPbeta prophage-derived uncharacterized protein YonE
G: SPbeta prophage-derived uncharacterized protein YonE
H: SPbeta prophage-derived uncharacterized protein YonE
I: SPbeta prophage-derived uncharacterized protein YonE
J: SPbeta prophage-derived uncharacterized protein YonE
K: SPbeta prophage-derived uncharacterized protein YonE
L: SPbeta prophage-derived uncharacterized protein YonE


Theoretical massNumber of molelcules
Total (without water)666,34112
Polymers666,34112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
SPbeta prophage-derived uncharacterized protein YonE


Mass: 55528.391 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spbetavirus SPbeta / Gene: yonE, BSU21120 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O31953
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: YonE portal protein from SPbeta phage / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Spbetavirus SPbeta
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22320 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00230828
ELECTRON MICROSCOPYf_angle_d0.49241592
ELECTRON MICROSCOPYf_dihedral_angle_d4.6313924
ELECTRON MICROSCOPYf_chiral_restr0.0354464
ELECTRON MICROSCOPYf_plane_restr0.0035280

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