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Open data
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Basic information
Entry | Database: PDB / ID: 7r2k | ||||||||||||
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Title | elongated Cascade complex from type I-A CRISPR-Cas system | ||||||||||||
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![]() | ANTIVIRAL PROTEIN / elongated Cascade complex / cascade / type I-A / genome editing | ||||||||||||
Function / homology | ![]() exonuclease activity / endonuclease activity / defense response to virus / nucleic acid binding / RNA helicase activity / Hydrolases; Acting on ester bonds / hydrolase activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Hu, C. / Ni, D. / Nam, K.H. / Terns, M. / Stahlberg, H. / Ke, A. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural snapshots for an atypic type I CRISPR-Cas system Authors: Ni, D. / Hu, C. / Nam, K.H. / Terns, M. / Stahlberg, H. / Ke, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 954.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 14245MC ![]() 7r21C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-CRISPR-associated ... , 2 types, 2 molecules AQ
#1: Protein | Mass: 74475.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#5: Protein | Mass: 27130.014 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8U336, Hydrolases; Acting on ester bonds |
-Protein , 4 types, 19 molecules CEFGHIJKLMNOPRTVWSY
#2: Protein | Mass: 12208.933 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 36989.148 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #6: Protein | | Mass: 29147.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #9: Protein | | Mass: 38800.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules DX
#3: DNA chain | Mass: 2788.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#8: DNA chain | Mass: 1126.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain / Non-polymers , 2 types, 3 molecules U![](data/chem/img/NI.gif)
![](data/chem/img/NI.gif)
#10: Chemical | #7: RNA chain | | Mass: 18389.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-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 |
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Sample preparation
Component | Name: elongated Cascade complex from Pyrococcus furiosus type I-A CRISPR/Cas system Type: COMPLEX / Details: Cascade alone / Entity ID: #1-#9 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.55 MDa / Experimental value: YES |
Buffer solution | pH: 7.5 |
Buffer component | Conc.: 150 mM / Name: sodium chloride / Formula: NaCl |
Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: 4s force 0 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8500 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49699 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||
Refine LS restraints |
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