+Open data
-Basic information
Entry | Database: PDB / ID: 7yoj | |||||||||
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Title | Structure of CasPi with guide RNA and target DNA | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/DNA/RNA / CasPi complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Transposase Function and homology information | |||||||||
Biological species | Armatimonadota bacterium (bacteria) Armatimonadetes bacterium (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Li, C.P. / Wang, J. / Liu, J.J. | |||||||||
Funding support | China, 1items
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Citation | Journal: Cell Res / Year: 2023 Title: The compact Casπ (Cas12l) 'bracelet' provides a unique structural platform for DNA manipulation. Authors: Ao Sun / Cheng-Ping Li / Zhihang Chen / Shouyue Zhang / Dan-Yuan Li / Yun Yang / Long-Qi Li / Yuqian Zhao / Kaichen Wang / Zhaofu Li / Jinxia Liu / Sitong Liu / Jia Wang / Jun-Jie Gogo Liu / Abstract: CRISPR-Cas modules serve as the adaptive nucleic acid immune systems for prokaryotes, and provide versatile tools for nucleic acid manipulation in various organisms. Here, we discovered a new ...CRISPR-Cas modules serve as the adaptive nucleic acid immune systems for prokaryotes, and provide versatile tools for nucleic acid manipulation in various organisms. Here, we discovered a new miniature type V system, CRISPR-Casπ (Cas12l) (~860 aa), from the environmental metagenome. Complexed with a large guide RNA (~170 nt) comprising the tracrRNA and crRNA, Casπ (Cas12l) recognizes a unique 5' C-rich PAM for DNA cleavage under a broad range of biochemical conditions, and generates gene editing in mammalian cells. Cryo-EM study reveals a 'bracelet' architecture of Casπ effector encircling the DNA target at 3.4 Å resolution, substantially different from the canonical 'two-lobe' architectures of Cas12 and Cas9 nucleases. The large guide RNA serves as a 'two-arm' scaffold for effector assembly. Our study expands the knowledge of DNA targeting mechanisms by CRISPR effectors, and offers an efficient but compact platform for DNA manipulation. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yoj.cif.gz | 303.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yoj.ent.gz | 231.2 KB | Display | PDB format |
PDBx/mmJSON format | 7yoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yoj_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7yoj_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7yoj_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 7yoj_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/7yoj ftp://data.pdbj.org/pub/pdb/validation_reports/yo/7yoj | HTTPS FTP |
-Related structure data
Related structure data | 33983MC 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: 98731.234 Da / Num. of mol.: 1 / Mutation: D537A, E643A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Armatimonadota bacterium (bacteria) / Gene: DCC45_12200, EDM73_08925 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A399WQY8 |
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#2: DNA chain | Mass: 3688.405 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Armatimonadetes bacterium (bacteria) / Production host: Escherichia coli (E. coli) |
#3: DNA chain | Mass: 9192.878 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Armatimonadetes bacterium (bacteria) / Production host: Escherichia coli (E. coli) |
#4: RNA chain | Mass: 56411.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Armatimonadetes bacterium (bacteria) / Production host: Escherichia coli (E. coli) |
-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: CasPi / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.17728 MDa / Experimental value: NO |
Source (natural) | Organism: Armatimonadetes bacterium (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-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 magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Image processing |
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CTF correction |
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Symmetry |
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