6I1K

Crystal structure of catalytically inactive FnCas12a in complex with a crRNA guide and a dsDNA target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a.

Swarts, D.C.Jinek, M.

(2019) Mol. Cell 73: 589-600.e4

  • DOI: 10.1016/j.molcel.2018.11.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CRISPR-Cas12a (Cpf1) is an RNA-guided DNA-cutting nuclease that has been repurposed for genome editing. Upon target DNA binding, Cas12a cleaves both the target DNA in cis and non-target single-stranded DNAs (ssDNAs) in trans. To elucidate the molecul ...

    CRISPR-Cas12a (Cpf1) is an RNA-guided DNA-cutting nuclease that has been repurposed for genome editing. Upon target DNA binding, Cas12a cleaves both the target DNA in cis and non-target single-stranded DNAs (ssDNAs) in trans. To elucidate the molecular basis for both DNase cleavage modes, we performed structural and biochemical studies on Francisella novicida Cas12a. We show that guide RNA-target strand DNA hybridization conformationally activates Cas12a, triggering its trans-acting, non-specific, single-stranded DNase activity. In turn, cis cleavage of double-stranded DNA targets is a result of protospacer adjacent motif (PAM)-dependent DNA duplex unwinding, electrostatic stabilization of the displaced non-target DNA strand, and ordered sequential cleavage of the non-target and target DNA strands. Cas12a releases the PAM-distal DNA cleavage product and remains bound to the PAM-proximal DNA cleavage product in a catalytically competent, trans-active state. Together, these results provide a revised model for the molecular mechanisms of both the cis- and the trans-acting DNase activities of Cas12a enzymes, enabling their further exploitation as genome editing tools.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland. Electronic address: jinek@bioc.uzh.ch.,Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas12a
A
1302Francisella tularensis subsp. novicida (strain U112)Mutation(s): 0 
Gene Names: cas12a (cpf1)
EC: 3.1.21.1, 4.6.1.22
Find proteins for A0Q7Q2 (Francisella tularensis subsp. novicida (strain U112))
Go to UniProtKB:  A0Q7Q2
Entity ID: 2
MoleculeChainsLengthOrganism
crRNA (40-MER)B40synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA target strand (38-MER)C38synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA non-target strand (33-MER)D38synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.172α = 90.00
b = 141.681β = 97.43
c = 89.478γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationGermanyALTF 179-2015
European Molecular Biology OrganizationGermanyaALTF 509-2017
Swiss National Science FoundationSwitzerlandSNSF 31003A_149393

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references