6I1K | pdb_00006i1k

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

• PDB DOI: https://doi.org/10.2210/pdb6I1K/pdb
• NAKB: 6I1K

• Classification: HYDROLASE
• Organism(s): Francisella tularensis subsp. novicida U112, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-29 Released: 2019-01-23 
• Deposition Author(s): Jinek, M., Swarts, D.C.
• Funding Organization(s): European Molecular Biology Organization, Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.264 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

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

• PubMed: 30639240 
• DOI: https://doi.org/10.1016/j.molcel.2018.11.021
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 189.46 kDa 
• Atom Count: 12,982 
• Modeled Residue Count: 1,393 
• Deposited Residue Count: 1,418 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas12a	A	1,302	Francisella tularensis subsp. novicida U112	Mutation(s): 0  Gene Names: cas12a, cpf1, FTN_1397 EC: 3.1.21.1 (PDB Primary Data), 3.1.27.2 (PDB Primary Data), 4.6.1.22 (UniProt)
UniProt
Find proteins for A0Q7Q2 (Francisella tularensis subsp. novicida (strain ATCC 15482 / CCUG 33449 / U112)) Explore A0Q7Q2  Go to UniProtKB:  A0Q7Q2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
crRNA (40-MER)	B	40	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA target strand (38-MER)	C	38	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA non-target strand (33-MER)	D	38	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	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	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 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.172	α = 90
b = 141.681	β = 97.43
c = 89.478	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
Coot	model building
XSCALE	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Jinek, M., Swarts, D.C.

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Funding Organization	Location	Grant Number
European Molecular Biology Organization	Germany	ALTF 179-2015
European Molecular Biology Organization	Germany	aALTF 509-2017
Swiss National Science Foundation	Switzerland	SNSF 31003A_149393

Revision History  

• 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
• Version 1.3: 2024-10-09
  Changes: Structure summary