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- EMDB-41281: CryoEM structure of Shedu from Bacillus cereus -

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Basic information

Entry
Database: EMDB / ID: EMD-41281
TitleCryoEM structure of Shedu from Bacillus cereus
Map dataCryoEM structure of Shedu from Bacillus cereus
Sample
  • Complex: Bacillus cereus Shedu Tetramer
    • Protein or peptide: Shedu protein SduA
KeywordsShedu / DUF4263 / Bacterial defense systems / Nuclease / Anti-plasmid defense system / PD-(D/E)XK nuclease / Whirly domain / Two-component signaling / DNA BINDING PROTEIN
Function / homologyProtein of unknown function DUF4263 / : / Shedu protein SduA, C-terminal / Shedu protein SduA, N-terminal / nuclease activity / defense response to virus / Shedu protein SduA
Function and homology information
Biological speciesBacillus cereus B4264 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGu Y / Corbett K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R35 GM144121 United States
CitationJournal: Mol Cell / Year: 2025
Title: Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains.
Authors: Yajie Gu / Huan Li / Amar Deep / Eray Enustun / Dapeng Zhang / Kevin D Corbett /
Abstract: Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease. Here, we reveal the structural basis for activation of Bacillus cereus Shedu. Two ...Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease. Here, we reveal the structural basis for activation of Bacillus cereus Shedu. Two cryoelectron microscopy structures of Shedu show that it switches between inactive and active states through conformational changes affecting active-site architecture, which are controlled by the protein's N-terminal domain (NTD). We find that B. cereus Shedu cleaves near DNA ends with a 3' single-stranded overhang, likely enabling it to specifically degrade the DNA injected by certain bacteriophages. Bioinformatic analysis of Shedu homologs reveals a conserved nuclease domain with remarkably diverse N-terminal regulatory domains: we identify 79 distinct NTD types falling into eight broad classes, including those with predicted nucleic acid binding, enzymatic, and other activities. Together, these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs that likely respond to a range of signals.
History
DepositionJul 19, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41281.png

Downloads & links

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Map

FileDownload / File: emd_41281.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of Shedu from Bacillus cereus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.23003 - 0.6241807
Average (Standard dev.)-0.0002845068 (±0.011196711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_41281_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_41281_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus cereus Shedu Tetramer

EntireName: Bacillus cereus Shedu Tetramer
Components
  • Complex: Bacillus cereus Shedu Tetramer
    • Protein or peptide: Shedu protein SduA

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Supramolecule #1: Bacillus cereus Shedu Tetramer

SupramoleculeName: Bacillus cereus Shedu Tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus cereus B4264 (bacteria)
Molecular weightTheoretical: 175 KDa

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Macromolecule #1: Shedu protein SduA

MacromoleculeName: Shedu protein SduA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus cereus B4264 (bacteria)
Molecular weightTheoretical: 44.016969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNASDKINVW TTSRDSAVCG DIELKKTSTT RLIFRPEIVN NNKNPKASVR GCFIFQKKGR NALWDDYKEL DMNKLKAEEW IKLEINSDA MLTLTKEIQK HYAVHEKYGV RYGAFHLFKD NPDIEKLIEM FESNTDLLTQ LMEDDKSEAL EKTLEWIVTN D NPDKIIDR ...String:
SNASDKINVW TTSRDSAVCG DIELKKTSTT RLIFRPEIVN NNKNPKASVR GCFIFQKKGR NALWDDYKEL DMNKLKAEEW IKLEINSDA MLTLTKEIQK HYAVHEKYGV RYGAFHLFKD NPDIEKLIEM FESNTDLLTQ LMEDDKSEAL EKTLEWIVTN D NPDKIIDR LKNLKEQDLD QLNTLIGIAN LKKVLSVWES NKLTNTSEKF WQSVLKENTW ILSQIFSNPT VLINDEAYVG GK TVKNDSG KLVDFLYANP FSKDAVLIEI KTPSTPLITP TEYRTGVYSA HKDLTGAVTQ VLTYKTTLQR EYQNIDYNNY RQG IKTDFD IITPCCVVIA GMFDTLTDTA HRHSFELYRK ELKNVTVITF DELFERVKGL IKLLEG

UniProtKB: Shedu protein SduA

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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

Concentration0.79 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
300.0 mMNaClSodium Chloride
20.0 mMC4H11NO3tris(hydroxymethyl)aminomethane
1.0 mMC4H10O2S2Dithiothreitol
5.0 mMMgCl2Magnesium Chloride

Details: Prepared using deionized water and filtered strelized.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsFreshly collected from size-exclusion column

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Details: non-uniform refinement from cryoSPARC / Number images used: 149464
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8ti8:
CryoEM structure of Shedu from Bacillus cereus

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