6W64 | pdb_00006w64

Cryo-EM structure of Cas12i-crRNA-dsDNA complex in I1 state

• PDB DOI: https://doi.org/10.2210/pdb6W64/pdb
• EM Map EMD-21552: EMDB EMDataResource
• NAKB: 6W64

• Classification: HYDROLASE/DNA/RNA
• Organism(s): Lachnospiraceae bacterium ND2006
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-16 Released: 2020-09-16 
• Deposition Author(s): Chang, L., Li, Z., Zhang, H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanisms for target recognition and cleavage by the Cas12i RNA-guided endonuclease.

Zhang, H., Li, Z., Xiao, R., Chang, L.

(2020) Nat Struct Mol Biol 27: 1069-1076

• PubMed: 32895556 
• DOI: https://doi.org/10.1038/s41594-020-0499-0
• Primary Citation Related Structures: 
  6W5C, 6W62, 6W64


• PubMed Abstract: 
  

  Cas12i is a recently identified type V CRISPR-Cas endonuclease that predominantly cleaves the non-target strand of a double-stranded DNA substrate. This nicking activity of Cas12i could potentially be used for genome editing with high specificity. To elucidate its mechanisms for target recognition and cleavage, we determined cryo-EM structures of Cas12i in multiple functional states. Cas12i pre-orders a seven-nucleotide seed sequence of the crRNA for target recognition and undergoes a two-step activation through crRNA-DNA hybridization. Formation of 14 base pairs activates the nickase activity, and 28-bp hybridization promotes cleavage of the target strand. The atomic structures and mechanistic insights gained should facilitate the manipulation of Cas12i for genome editing applications.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, IN, USA. [e-mail].
Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Department of Biological Sciences, Purdue University, West Lafayette, IN, USA. [e-mail].
Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 145.58 kDa 
• Atom Count: 8,505 
• Modeled Residue Count: 984 
• Deposited Residue Count: 1,155 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas12i	A	1,092	Lachnospiraceae bacterium ND2006	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
crRNA	B	38	Lachnospiraceae bacterium ND2006

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	C	25	Lachnospiraceae bacterium ND2006

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Chang, L., Li, Z., Zhang, H.

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references