+Open data
-Basic information
Entry | Database: PDB / ID: 8inb | ||||||
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Title | Cryo-EM structure of Cas12j-SF05-crRNA-dsDNA complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA/DNA / CRISPR / RNA BINDING PROTEIN-RNA complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex | ||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Biggievirus Mos11 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Zhang, X. / Duan, Z.Q. / Zhu, J.K. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2023 Title: Molecular basis for DNA cleavage by the hypercompact Cas12j-SF05. Authors: Zhiqiang Duan / Xi Zhang / Jun-Tao Zhang / Shanshan Li / Ruiheng Liu / Jie Sun / Qingzhi Zhao / Nannan Jia / Ning Jia / Jian-Kang Zhu / | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8inb.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8inb.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 8inb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8inb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8inb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8inb_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 8inb_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/8inb ftp://data.pdbj.org/pub/pdb/validation_reports/in/8inb | HTTPS FTP |
-Related structure data
Related structure data | 35595MC 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: Protein | Mass: 83449.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Biggievirus Mos11 / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: RNA chain | Mass: 18179.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Biggievirus Mos11 |
#3: DNA chain | Mass: 16994.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Biggievirus Mos11 |
#4: DNA chain | Mass: 16900.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Biggievirus Mos11 |
-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: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Biggievirus Mos11 |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.4 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59719 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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