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Open data
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Basic information
Entry | Database: PDB / ID: 6ny2 | |||||||||
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Title | CasX-gRNA-DNA(45bp) state I | |||||||||
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![]() | RNA BINDING PROTEIN/RNA/DNA / CasX / sgRNA / target DNA / CRISPR / RNA BINDING PROTEIN-RNA-DNA complex | |||||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Transposase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Liu, J.J. / Orlova, N. / Nogales, E. / Doudna, J.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CasX enzymes comprise a distinct family of RNA-guided genome editors. Authors: Jun-Jie Liu / Natalia Orlova / Benjamin L Oakes / Enbo Ma / Hannah B Spinner / Katherine L M Baney / Jonathan Chuck / Dan Tan / Gavin J Knott / Lucas B Harrington / Basem Al-Shayeb / ...Authors: Jun-Jie Liu / Natalia Orlova / Benjamin L Oakes / Enbo Ma / Hannah B Spinner / Katherine L M Baney / Jonathan Chuck / Dan Tan / Gavin J Knott / Lucas B Harrington / Basem Al-Shayeb / Alexander Wagner / Julian Brötzmann / Brett T Staahl / Kian L Taylor / John Desmarais / Eva Nogales / Jennifer A Doudna / ![]() ![]() Abstract: The RNA-guided CRISPR-associated (Cas) proteins Cas9 and Cas12a provide adaptive immunity against invading nucleic acids, and function as powerful tools for genome editing in a wide range of ...The RNA-guided CRISPR-associated (Cas) proteins Cas9 and Cas12a provide adaptive immunity against invading nucleic acids, and function as powerful tools for genome editing in a wide range of organisms. Here we reveal the underlying mechanisms of a third, fundamentally distinct RNA-guided genome-editing platform named CRISPR-CasX, which uses unique structures for programmable double-stranded DNA binding and cleavage. Biochemical and in vivo data demonstrate that CasX is active for Escherichia coli and human genome modification. Eight cryo-electron microscopy structures of CasX in different states of assembly with its guide RNA and double-stranded DNA substrates reveal an extensive RNA scaffold and a domain required for DNA unwinding. These data demonstrate how CasX activity arose through convergent evolution to establish an enzyme family that is functionally separate from both Cas9 and Cas12a. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244.8 KB | Display | ![]() |
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PDB format | ![]() | 192.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.8 KB | Display | ![]() |
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Full document | ![]() | 814.5 KB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 51.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8996MC ![]() 8980C ![]() 8987C ![]() 8988C ![]() 8989C ![]() 8990C ![]() 8991C ![]() 8994C ![]() 6ny1C ![]() 6ny3C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: DNA chain | Mass: 13823.874 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: DNA chain | Mass: 13742.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Protein | Mass: 108092.836 Da / Num. of mol.: 1 / Mutation: D672A, E769A, D935A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: DD725_10130 / Production host: ![]() ![]() |
#4: RNA chain | Mass: 39272.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
Sequence details | The CasX construct has the following sequence: ...The CasX construct has the following sequence: SNAMEKRINK |
-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: CasX-gRNA-DNA(45bp) state I / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
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 |
Image recording | Electron dose: 46 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149361 / Symmetry type: POINT |