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 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.molcel.2018.11.021
  • Primary Citation of Related Structures:  
    6I1K, 6I1L

  • 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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas12a1,302Francisella tularensis subsp. novicida U112Mutation(s): 0 
Gene Names: cas12acpf1FTN_1397
EC: 3.1.21.1 (PDB Primary Data), 3.1.27.2 (PDB Primary Data)
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
crRNA (40-MER)40synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA target strand (38-MER)38synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA non-target strand (33-MER)38synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
N [auth A]
O [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
S [auth B],
T [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.172α = 90
b = 141.681β = 97.43
c = 89.478γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Cootmodel building
XSCALEdata scaling

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description