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Yorodumi- PDB-8j12: Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j12 | ||||||
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Title | Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/DNA/RNA / CRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA complex | ||||||
Function / homology | Function and homology information endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Acidibacillus sulfuroxidans (bacteria) Acidibacillus sulfooxidans (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||
Authors | 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 | Japan, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j12.cif.gz | 284.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j12.ent.gz | 214.9 KB | Display | PDB format |
PDBx/mmJSON format | 8j12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j12_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8j12_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8j12_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 8j12_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/8j12 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/8j12 | HTTPS FTP |
-Related structure data
Related structure data | 35912MC 8j1jC 8j3rC 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
-DNA chain , 2 types, 2 molecules DE
#2: DNA chain | Mass: 11694.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidibacillus sulfooxidans (bacteria) / Production host: Escherichia coli (E. coli) |
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#3: DNA chain | Mass: 11689.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidibacillus sulfooxidans (bacteria) / Production host: Escherichia coli (E. coli) |
-Protein / RNA chain , 2 types, 3 molecules ABC
#1: Protein | Mass: 49925.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidibacillus sulfuroxidans (bacteria) / Gene: BM613_13600 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U3D0N8 #4: RNA chain | | Mass: 72329.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidibacillus sulfooxidans (bacteria) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 2 types, 9 molecules
#5: Chemical | ChemComp-MG / #6: Chemical | |
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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 |
-Sample preparation
Component | Name: AsCas12f-sgRNA-target DNA / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mycolicibacterium mucogenicum (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
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) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79011 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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