5NFV

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


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Literature

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: 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 ...

    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. Electronic address: jinek@bioc.uzh.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cpf1A1302Francisella tularensis subsp. novicida U112Mutation(s): 2 
Gene Names: cpf1, FTN_1397, cas12a
EC: 3.1 (PDB Primary Data), 3.1.21.1 (UniProt), 4.6.1.22 (UniProt)
UniProt
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
pre-crRNAB 46synthetic construct
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA target strandC 38synthetic construct
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA non-target strandD 38synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P
Download Ideal Coordinates CCD File 
G [auth A]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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E [auth A],
F [auth A],
H [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
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
PHENIXrefinement
XDSdata reduction
PHASERphasing
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