+Open data
-Basic information
Entry | Database: PDB / ID: 8fuk | |||||||||
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Title | V. cholerae TniQ-Cascade complex with Type III-B crRNA | |||||||||
Components |
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Keywords | ANTIVIRAL PROTEIN/RNA / Type I-F CAST / DNA Transposition / CRISPR Transposon / ANTIVIRAL PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | metagenome (others) Vibrio cholerae (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Chou, C.W. / Finkelstein, I.J. / Hu, K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be Published Title: V. cholerae TniQ-Cascade complex with Type III-B crRNA Authors: Chou, C.W. / Finkelstein, I.J. / Hu, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fuk.cif.gz | 729.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fuk.ent.gz | 476.4 KB | Display | PDB format |
PDBx/mmJSON format | 8fuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fuk_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8fuk_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8fuk_validation.xml.gz | 91.4 KB | Display | |
Data in CIF | 8fuk_validation.cif.gz | 138.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/8fuk ftp://data.pdbj.org/pub/pdb/validation_reports/fu/8fuk | HTTPS FTP |
-Related structure data
Related structure data | 29459MC M: map data used to model this data C: citing same article (ref.) |
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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: RNA chain | Mass: 19333.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||||
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#2: Protein | Mass: 39886.031 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: csy3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6I8WFX5 #3: Protein | | Mass: 72294.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: FXE93_08750 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFX4 #4: Protein | | Mass: 23130.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: cas6f / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFX3 #5: Protein | Mass: 45597.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: FXE93_08745 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFX7 |
-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: Type I-F TniQ-Cascade with Type III-B crRNA / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.45 MDa / Experimental value: NO |
Source (natural) | Organism: Vibrio cholerae (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21 (DE3) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 39.2 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1235 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67000 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.01 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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