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- PDB-8ti9: CryoEM structure of octamer assembly of Shedu nuclease domain fro... -

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Basic information

Entry
Database: PDB / ID: 8ti9
TitleCryoEM structure of octamer assembly of Shedu nuclease domain from Bacillus cereus
ComponentsShedu protein SduA
KeywordsDNA BINDING PROTEIN / Shedu / DUF4263 / Bacterial defense systems / Nuclease / Anti-plasmid defense system / PD-(D/E)XK nuclease / Whirly domain / Two-component signaling
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsGu, Y. / Corbett, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R35 GM144121 United States
CitationJournal: to be published
Title: Shedu anti-phage nucleases share a common enzymatic core regulated by diverse sensor domains
Authors: Gu, Y. / Corbett, K.
History
DepositionJul 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Shedu protein SduA
F: Shedu protein SduA
G: Shedu protein SduA
H: Shedu protein SduA
A: Shedu protein SduA
B: Shedu protein SduA
C: Shedu protein SduA
D: Shedu protein SduA


Theoretical massNumber of molelcules
Total (without water)209,8948
Polymers209,8948
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Shedu protein SduA / Putative nuclease SduA


Mass: 26236.760 Da / Num. of mol.: 8 / Mutation: E264A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus B4264 (bacteria) / Gene: sduA, BCB4264_A0974 / Production host: Escherichia coli (E. coli) / References: UniProt: B7HFR2

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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: Bacillus cereus Shedu delta_NL octamer / Type: COMPLEX
Details: Octamer assembly of Bacillus cereus Shedu nuclease domain, which truncates the N-terminal and linker region. Glutamic acid 264 is mutated to Alanine.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.216 MDa / Experimental value: YES
Source (natural)Organism: Bacillus cereus B4264 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Details: Prepared using deionized water and filtered strelized.
Buffer component
IDConc.NameFormulaBuffer-ID
1500 mMSodium ChlorideNaCl1
220 mMHEPESC8H18N2O4S1
31 mMDithiothreitolC4H10O2S21
45 mMMagnesium ChlorideMgCl21
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Freshly collected from size-exclusion column
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARC4.2.1CTF correction
7Coot0.9.6model fitting
12cryoSPARC4.2.13D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138326 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212736
ELECTRON MICROSCOPYf_angle_d0.35717314
ELECTRON MICROSCOPYf_dihedral_angle_d9.3214630
ELECTRON MICROSCOPYf_chiral_restr0.042068
ELECTRON MICROSCOPYf_plane_restr0.0032146

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