Crystal structure of catalytically inactive FnCas12 mutant bound to an R-loop structure containing a pre-crRNA mimic and full-length DNA target

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.

Swarts, D.C.van der Oost, J.Jinek, M.

(2017) Mol Cell 66: 221-233.e4

  • DOI: https://doi.org/10.1016/j.molcel.2017.03.016
  • Primary Citation of Related Structures:  
    5NFV, 5NG6

  • PubMed Abstract: 

    The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding. Furthermore, the R-loop complex structure reveals the strand displacement mechanism that facilitates guide-target hybridization and suggests a mechanism for double-stranded DNA cleavage involving a single active site. Together, these insights advance our mechanistic understanding of Cas12a enzymes and may contribute to further development of genome editing technologies.

  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cpf11,302Francisella tularensis subsp. novicida U112Mutation(s): 2 
Gene Names: cpf1FTN_1397
EC: 3.1
Find proteins for A0Q7Q2 (Francisella tularensis subsp. novicida (strain U112))
Explore A0Q7Q2 
Go to UniProtKB:  A0Q7Q2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0Q7Q2
Sequence Annotations
  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
pre-crRNA46synthetic construct
Sequence Annotations
  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA target strand38synthetic construct
Sequence Annotations
  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA non-target strand38synthetic construct
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.421α = 90
b = 143.703β = 94.16
c = 84.628γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_149393

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release