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Yorodumi- PDB-8ti9: CryoEM structure of octamer assembly of Shedu nuclease domain fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ti9 | ||||||
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Title | CryoEM structure of octamer assembly of Shedu nuclease domain from Bacillus cereus | ||||||
Components | Shedu protein SduA | ||||||
Keywords | DNA BINDING PROTEIN / Shedu / DUF4263 / Bacterial defense systems / Nuclease / Anti-plasmid defense system / PD-(D/E)XK nuclease / Whirly domain / Two-component signaling | ||||||
Function / homology | Protein 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 species | Bacillus cereus B4264 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å | ||||||
Authors | Gu, Y. / Corbett, K. | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Shedu anti-phage nucleases share a common enzymatic core regulated by diverse sensor domains Authors: Gu, Y. / Corbett, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ti9.cif.gz | 308.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ti9.ent.gz | 252.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ti9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ti9_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ti9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ti9_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 8ti9_validation.cif.gz | 84.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/8ti9 ftp://data.pdbj.org/pub/pdb/validation_reports/ti/8ti9 | HTTPS FTP |
-Related structure data
Related structure data | 41282MC 8ti8C 8tiaC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 | |||||||||||||||||||||||||
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Molecular weight | Value: 0.216 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Bacillus cereus B4264 (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Prepared using deionized water and filtered strelized. | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Freshly collected from size-exclusion column | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 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 building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
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