6GTG

Transition state structure of Cpf1(Cas12a) I4 conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity.

Stella, S.Mesa, P.Thomsen, J.Paul, B.Alcon, P.Jensen, S.B.Saligram, B.Moses, M.E.Hatzakis, N.S.Montoya, G.

(2018) Cell 175: 1856-1871.e21

  • DOI: 10.1016/j.cell.2018.10.045
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cas12a, also known as Cpf1, is a type V-A CRISPR-Cas RNA-guided endonuclease that is used for genome editing based on its ability to generate specific dsDNA breaks. Here, we show cryo-EM structures of intermediates of the cleavage reaction, thus visu ...

    Cas12a, also known as Cpf1, is a type V-A CRISPR-Cas RNA-guided endonuclease that is used for genome editing based on its ability to generate specific dsDNA breaks. Here, we show cryo-EM structures of intermediates of the cleavage reaction, thus visualizing three protein regions that sense the crRNA-DNA hybrid assembly triggering the catalytic activation of Cas12a. Single-molecule FRET provides the thermodynamics and kinetics of the conformational activation leading to phosphodiester bond hydrolysis. These findings illustrate why Cas12a cuts its target DNA and unleashes unspecific cleavage activity, degrading ssDNA molecules after activation. In addition, we show that other crRNAs are able to displace the R-loop inside the protein after target DNA cleavage, terminating indiscriminate ssDNA degradation. We propose a model whereby the conformational activation of the enzyme results in indiscriminate ssDNA cleavage. The displacement of the R-loop by a new crRNA molecule will reset Cas12a specificity, targeting new DNAs.


    Organizational Affiliation

    Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark. Electronic address: guillermo.montoya@cpr.ku.dk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas12a
A
1329Francisella tularensis subsp. novicida U112Mutation(s): 1 
Gene Names: cas12acpf1FTN_1397
EC: 3.1.21.1 (PDB Primary Data), 3.1.27.2 (PDB Primary Data), 4.6.1.22 (UniProt)
Find proteins for A0Q7Q2 (Francisella tularensis subsp. novicida (strain U112))
Go to UniProtKB:  A0Q7Q2

Find similar proteins by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
RNA (40-MER)B43Francisella tularensis subsp. novicida U112

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
DNA (32-MER)C55Francisella tularensis subsp. novicida U112

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*GP*AP*GP*CP*TP*CP*GP*TP*TP*AP*GP*AP*GP*AP*AP*GP*T)-3')D55Francisella tularensis subsp. novicida U112
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF14CC0001

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-18
    Changes: Other