7V93 | pdb_00007v93

Cryo-EM structure of the Cas12c2-sgRNA binary complex

• PDB DOI: https://doi.org/10.2210/pdb7V93/pdb
• EM Map EMD-31807: EMDB EMDataResource
• NAKB: 7V93

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): uncultured archaeon
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-24 Released: 2022-04-13 
• Deposition Author(s): Kurihara, N., Hirano, H., Tomita, A., Kobayashi, K., Kusakizako, T., Nishizawa, T., Yamashita, K., Nishimasu, H., Nureki, O.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the type V-C CRISPR-Cas effector enzyme.

Kurihara, N., Nakagawa, R., Hirano, H., Okazaki, S., Tomita, A., Kobayashi, K., Kusakizako, T., Nishizawa, T., Yamashita, K., Scott, D.A., Nishimasu, H., Nureki, O.

(2022) Mol Cell 82: 1865-1877.e4

• PubMed: 35366394 
• DOI: https://doi.org/10.1016/j.molcel.2022.03.006
• Primary Citation Related Structures: 
  7V93, 7V94


• PubMed Abstract: 
  

  RNA-guided CRISPR-Cas nucleases are widely used as versatile genome-engineering tools. Recent studies identified functionally divergent type V Cas12 family enzymes. Among them, Cas12c2 binds a CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA) and recognizes double-stranded DNA targets with a short TN PAM. Here, we report the cryo-electron microscopy structures of the Cas12c2-guide RNA binary complex and the Cas12c2-guide RNA-target DNA ternary complex. The structures revealed that the crRNA and tracrRNA form an unexpected X-junction architecture, and that Cas12c2 recognizes a single T nucleotide in the PAM through specific hydrogen-bonding interactions with two arginine residues. Furthermore, our biochemical analyses indicated that Cas12c2 processes its precursor crRNA to a mature crRNA using the RuvC catalytic site through a unique mechanism. Collectively, our findings improve the mechanistic understanding of diverse type V CRISPR-Cas effectors.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
PeptiDream Inc., 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa Prefecture 210-0821, Japan.
Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan.
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Arbor Biotechnologies, Cambridge, MA 02139, USA.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan; Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto 600-8411, Japan. Electronic address: [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: [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: 174.5 kDa 
• Atom Count: 8,792 
• Modeled Residue Count: 999 
• Deposited Residue Count: 1,344 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cas12c2	A	1,232	uncultured archaeon	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
sgRNA	B	112	uncultured archaeon

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3
MODEL REFINEMENT	REFMAC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Kurihara, N., Hirano, H., Tomita, A., Kobayashi, K., Kusakizako, T., Nishizawa, T., Yamashita, K., Nishimasu, H., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2022-06-01
  Changes: Database references
• Version 1.2: 2024-06-12
  Changes: Data collection, Refinement description