7ODF

Structure of the mini-RNA-guided endonuclease CRISPR-Cas_phi3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the mini-RNA-guided endonuclease CRISPR-Cas12j3.

Carabias, A.Fuglsang, A.Temperini, P.Pape, T.Sofos, N.Stella, S.Erlendsson, S.Montoya, G.

(2021) Nat Commun 12: 4476-4476

  • DOI: https://doi.org/10.1038/s41467-021-24707-3
  • Primary Citation of Related Structures:  
    7ODF

  • PubMed Abstract: 

    CRISPR-Cas12j is a recently identified family of miniaturized RNA-guided endonucleases from phages. These ribonucleoproteins provide a compact scaffold gathering all key activities of a genome editing tool. We provide the first structural insight into the Cas12j family by determining the cryoEM structure of Cas12j3/R-loop complex after DNA cleavage. The structure reveals the machinery for PAM recognition, hybrid assembly and DNA cleavage. The crRNA-DNA hybrid is directed to the stop domain that splits the hybrid, guiding the T-strand towards the catalytic site. The conserved RuvC insertion is anchored in the stop domain and interacts along the phosphate backbone of the crRNA in the hybrid. The assembly of a hybrid longer than 12-nt activates catalysis through key functional residues in the RuvC insertion. Our findings suggest why Cas12j unleashes unspecific ssDNA degradation after activation. A site-directed mutagenesis analysis supports the DNA cutting mechanism, providing new avenues to redesign CRISPR-Cas12j nucleases for genome editing.


  • Organizational Affiliation

    Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Copenhagen, Denmark.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cas_phi3766Phage #DMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*AP*TP*CP*CP*CP*AP*TP*TP*AP*CP*CP*AP*GP*CP*TP*GP*AP*AP*TP*TP*AP*C)-3')B [auth E]24synthetic construct
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*AP*AP*TP*TP*CP*AP*G)-3')C [auth G]9synthetic construct
Sequence Annotations
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*G)-3')D [auth C]2synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (43-MER)E [auth F]43synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF14CC0001
Novo Nordisk FoundationDenmarkNNF0024386
Novo Nordisk FoundationDenmarkNNF17SA0030214
Novo Nordisk FoundationDenmarkNNF18OC0055061

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2024-07-10
    Changes: Data collection, Refinement description