6LTR

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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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: https://doi.org/10.1038/s41467-020-19072-6
  • Primary Citation of Related Structures:  
    6LTP, 6LTR, 6LTU, 6LU0

  • 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 endonuclease that cleaves target dsDNA by an unknown mechanism ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cas12i2A1,055unidentifiedMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (56-mer)B56synthetic construct
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*TP*T)-3')C [auth D]13synthetic construct
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (35-MER)D [auth C]35synthetic construct
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Entity ID: 5
MoleculeChainsLengthOrganismImage
trans ssDNAE6synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.256α = 90
b = 123.025β = 90
c = 280.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

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