+Open data
-Basic information
Entry | Database: PDB / ID: 6vbw | ||||||
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Title | Cryo-EM structure of Cascade-TniQ-dsDNA ternary complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CRISPR-Cas system / Cascade- TniQ | ||||||
Function / homology | DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Jia, N. / Patel, D.J. | ||||||
Citation | Journal: Cell Res / Year: 2020 Title: Structure-function insights into the initial step of DNA integration by a CRISPR-Cas-Transposon complex. Authors: Ning Jia / Wei Xie / M Jason de la Cruz / Edward T Eng / Dinshaw J Patel / | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vbw.cif.gz | 643.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vbw.ent.gz | 522.2 KB | Display | PDB format |
PDBx/mmJSON format | 6vbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vbw_validation.pdf.gz | 837.2 KB | Display | wwPDB validaton report |
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Full document | 6vbw_full_validation.pdf.gz | 897.7 KB | Display | |
Data in XML | 6vbw_validation.xml.gz | 95.5 KB | Display | |
Data in CIF | 6vbw_validation.cif.gz | 152 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/6vbw ftp://data.pdbj.org/pub/pdb/validation_reports/vb/6vbw | HTTPS FTP |
-Related structure data
Related structure data | 21146MC 6v9pC 6v9qC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA chain , 2 types, 2 molecules ML
#1: DNA chain | Mass: 6685.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria) |
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#2: DNA chain | Mass: 30901.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria) |
-Protein , 4 types, 10 molecules ABCDFEGHIJ
#4: Protein | Mass: 72294.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) | ||||
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#5: Protein | Mass: 39886.031 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) #6: Protein | | Mass: 23130.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) #7: Protein | Mass: 45597.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) |
-RNA chain / Non-polymers , 2 types, 5 molecules K
#3: RNA chain | Mass: 19566.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria) |
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#8: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | N |
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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 |
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Molecular weight | Value: 0.4 MDa / Experimental value: YES | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 / Details: 20 mM HEPES, pH 7.5, 150 mM NaCl, 2 mM DTT | ||||||||||||||||||||||||
Buffer component | Formula: Tris | ||||||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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 |
Image recording | Electron dose: 2.16 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: RELION / Version: 2.1 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55900 / Symmetry type: POINT |