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- EMDB-71643: CryoEM structure of the YonE portal protein from Bacillus phage SPbeta -

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Basic information

Entry
Database: EMDB / ID: EMD-71643
TitleCryoEM structure of the YonE portal protein from Bacillus phage SPbeta
Map data
Sample
  • Complex: YonE portal protein from SPbeta phage
    • Protein or peptide: SPbeta prophage-derived uncharacterized protein YonE
KeywordsPortal protein / antiphage defence / VIRAL PROTEIN
Function / homologySPbeta prophage-derived uncharacterized protein YonE
Function and homology information
Biological speciesSpbetavirus SPbeta
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMishra BP / Ve T
Funding support Australia, 2 items
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, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71643.png

Downloads & links

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Map

FileDownload / File: emd_71643.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 336. Å		1.31 Å/pix.
x 256 pix.
= 336. Å		1.31 Å/pix.
x 256 pix.
= 336. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.138
Minimum - Maximum-0.48623037 - 0.81469536
Average (Standard dev.)0.00040832098 (±0.024310606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71643_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71643_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : YonE portal protein from SPbeta phage

EntireName: YonE portal protein from SPbeta phage
Components
  • Complex: YonE portal protein from SPbeta phage
    • Protein or peptide: SPbeta prophage-derived uncharacterized protein YonE

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Supramolecule #1: YonE portal protein from SPbeta phage

SupramoleculeName: YonE portal protein from SPbeta phage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Spbetavirus SPbeta

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Macromolecule #1: SPbeta prophage-derived uncharacterized protein YonE

MacromoleculeName: SPbeta prophage-derived uncharacterized protein YonE / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Spbetavirus SPbeta
Molecular weightTheoretical: 55.528391 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHSSG VDLGTENLYF QSNAEAEQLK NYFSNPDEFQ EEIEDLAQYF YISTAEIHQL FELIEALPTL NYKIDSFNKV KSSDKHISL LNKSLHKVKH KRLTRDLLKQ VATAGTLVGI WLGDAKSPYP FIFDEIKYVF PSFRRNGDWV CVVDMELFTK Y KDDQRNEL ...String:
MHHHHHHSSG VDLGTENLYF QSNAEAEQLK NYFSNPDEFQ EEIEDLAQYF YISTAEIHQL FELIEALPTL NYKIDSFNKV KSSDKHISL LNKSLHKVKH KRLTRDLLKQ VATAGTLVGI WLGDAKSPYP FIFDEIKYVF PSFRRNGDWV CVVDMELFTK Y KDDQRNEL LKSLSPYIKQ SDYENFMKDR EKYRFKELPQ ERTFPLRTGT LKRNQGLGTS WVTPGLYDVL HKKKLKDVER SI ANKIINA VAVLTIGTDK GNGEYTNMKL PKAVKQKIHG GVKTALEKNQ KDGVTVVSIP DFADINFPDV KADGLDGAKF DHI NSDIQS AYGLSGSLLN GDGGNYATSS LNLDTFYKRI GVLMEDIEQE VYQKLFNLVL PAAQKDNYYM NYDKDKPLTL KEKM DILIK LNDKGWSIKH VVDNLAGVSW ESYLEQTLYE TEELKLQEKI RPYQTSYTFT GNEVGRPNEG NKNNDNTVKS ATSNG NDNP I

UniProtKB: SPbeta prophage-derived uncharacterized protein YonE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22320
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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