6LTU

Crystal structure of Cas12i2 ternary complex with double Mg2+ bound in catalytic pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2.

Huang, X.Sun, W.Cheng, Z.Chen, M.Li, X.Wang, J.Sheng, G.Gong, W.Wang, Y.

(2020) Nat Commun 11: 5241-5241

  • DOI: 10.1038/s41467-020-19072-6
  • Primary Citation of Related Structures:  
    6LU0, 6LTP, 6LTR, 6LTU

  • PubMed Abstract: 
  • To understand how the RuvC catalytic domain of Class 2 Cas proteins cleaves DNA, it will be necessary to elucidate the structures of RuvC-containing Cas complexes in their catalytically competent states. Cas12i2 is a Class 2 type V-I CRISPR-Cas endon ...

    To understand how the RuvC catalytic domain of Class 2 Cas proteins cleaves DNA, it will be necessary to elucidate the structures of RuvC-containing Cas complexes in their catalytically competent states. Cas12i2 is a Class 2 type V-I CRISPR-Cas endonuclease that cleaves target dsDNA by an unknown mechanism. Here, we report structures of Cas12i2-crRNA-DNA complexes and a Cas12i2-crRNA complex. We reveal the mechanism of DNA recognition and cleavage by Cas12i2, and activation of the RuvC catalytic pocket induced by a conformational change of the Helical-II domain. The seed region (nucleotides 1-8) is dispensable for RuvC activation, but the duplex of the central spacer (nucleotides 9-15) is required. We captured the catalytic state of Cas12i2, with both metal ions and the ssDNA substrate bound in the RuvC catalytic pocket. Together, our studies provide significant insights into the DNA cleavage mechanism by RuvC-containing Cas proteins.


    Organizational Affiliation

    University of Chinese Academy of Sciences, 100049, Beijing, China. ylwang@ibp.ac.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cas12i2A1055unidentifiedMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (56-mer)B58synthetic construct
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*T)-3')D12synthetic construct
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    DNA (35-MER)C35synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 5
      MoleculeChainsLengthOrganismImage
      trans ssDNAE5synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      EDO
      Query on EDO

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

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.57 Å
      • R-Value Free: 0.229 
      • R-Value Work: 0.202 
      • R-Value Observed: 0.203 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 94.329α = 90
      b = 123.575β = 90
      c = 281.218γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Natural Science Foundation of China (NSFC)China31630015
      National Natural Science Foundation of China (NSFC)China31725008

      Revision History 

      • Version 1.0: 2020-10-28
        Type: Initial release
      • Version 1.1: 2020-11-04
        Changes: Database references