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Open data
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Basic information
Entry | Database: PDB / ID: 8j3r | ||||||
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Title | Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA | ||||||
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![]() | RNA BINDING PROTEIN/DNA/RNA / CRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX / RNA BINDING PROTEIN-DNA-RNA complex | ||||||
Function / homology | ![]() endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å | ||||||
![]() | Hino, T. / Omura, N.S. / Nakagawa, R. / Togashi, T. / Takeda, N.S. / Hiramoto, T. / Tasaka, S. / Hirano, H. / Tokuyama, T. / Uosaki, H. ...Hino, T. / Omura, N.S. / Nakagawa, R. / Togashi, T. / Takeda, N.S. / Hiramoto, T. / Tasaka, S. / Hirano, H. / Tokuyama, T. / Uosaki, H. / Ishiguro, H. / Yamano, H. / Ozaki, Y. / Motooka, D. / Mori, H. / Kirita, Y. / Kise, Y. / Itoh, Y. / Matoba, S. / Aburatani, H. / Yachie, N. / Siksnys, V. / Ohmori, T. / Hoshino, A. / Nureki, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Minimal and most efficient genome editing Cas enzyme Authors: Hino, T. / Omura, N.S. / Nakagawa, R. / Togashi, T. / Takeda, N.S. / Hiramoto, T. / Tasaka, S. / Hirano, H. / Tokuyama, T. / Uosaki, H. / Ishiguro, H. / Yamano, H. / Ozaki, Y. / Motooka, D. ...Authors: Hino, T. / Omura, N.S. / Nakagawa, R. / Togashi, T. / Takeda, N.S. / Hiramoto, T. / Tasaka, S. / Hirano, H. / Tokuyama, T. / Uosaki, H. / Ishiguro, H. / Yamano, H. / Ozaki, Y. / Motooka, D. / Mori, H. / Kirita, Y. / Kise, Y. / Itoh, Y. / Matoba, S. / Aburatani, H. / Yachie, N. / Siksnys, V. / Ohmori, T. / Hoshino, A. / Nureki, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.5 KB | Display | ![]() |
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PDB format | ![]() | 192.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.8 KB | Display | |
Data in CIF | ![]() | 55.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35965MC ![]() 8j12C ![]() 8j1jC M: map data used to model this data C: citing same article ( |
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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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Components
-DNA chain , 2 types, 2 molecules DE
#2: DNA chain | Mass: 11388.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#3: DNA chain | Mass: 11698.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
-Protein / RNA chain , 2 types, 3 molecules ABC
#1: Protein | Mass: 49978.141 Da / Num. of mol.: 2 / Mutation: I123H, D195K, D208R, V232A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BM613_13600 / Production host: ![]() ![]() #4: RNA chain | | Mass: 38287.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 2 types, 4 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#5: Chemical | ChemComp-ZN / |
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#6: Chemical |
-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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155198 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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