7VTN | pdb_00007vtn

Cryo-EM structure of the Cas13bt3-crRNA-target RNA ternary complex

• PDB DOI: https://doi.org/10.2210/pdb7VTN/pdb
• NAKB: 7VTN
• EM Map EMD-32118: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Planctomycetota bacterium, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-10-30 Released: 2022-09-07 
• Deposition Author(s): Nakagawa, R., Soumya, K., Han, A., Takeda, N.S., Tomita, A., Hirano, H., Kusakizako, T., Tomohiro, N., Yamashita, K., Feng, Z., 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: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and engineering of the minimal type VI CRISPR-Cas13bt3.

Nakagawa, R., Kannan, S., Altae-Tran, H., Takeda, S.N., Tomita, A., Hirano, H., Kusakizako, T., Nishizawa, T., Yamashita, K., Zhang, F., Nishimasu, H., Nureki, O.

(2022) Mol Cell 82: 3178-3192.e5

• PubMed: 36027912 
• DOI: https://doi.org/10.1016/j.molcel.2022.08.001
• Primary Citation Related Structures: 
  7VTI, 7VTN


• PubMed Abstract: 
  

  Type VI CRISPR-Cas13 effector enzymes catalyze RNA-guided RNA cleavage and have been harnessed for various technologies, such as RNA detection, targeting, and editing. Recent studies identified Cas13bt3 (also known as Cas13X.1) as a miniature Cas13 enzyme, which can be used for knockdown and editing of target transcripts in mammalian cells. However, the action mechanism of the compact Cas13bt3 remains unknown. Here, we report the structures of the Cas13bt3-guide RNA complex and the Cas13bt3-guide RNA-target RNA complex. The structures revealed how Cas13bt3 recognizes the guide RNA and its target RNA and provided insights into the activation mechanism of Cas13bt3, which is distinct from those of the other Cas13a/d enzymes. Furthermore, we rationally engineered enhanced Cas13bt3 variants and ultracompact RNA base editors. Overall, this study improves our mechanistic understanding of the CRISPR-Cas13 enzymes and paves the way for the development of efficient Cas13-mediated transcriptome modulation technologies.

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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.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, 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.

Macromolecule Content 

• Total Structure Weight: 118.09 kDa 
• Atom Count: 7,305 
• Modeled Residue Count: 768 
• Deposited Residue Count: 863 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas13bt3	A	777	Planctomycetota bacterium	Mutation(s): 4  Gene Names: DRP66_05270
UniProt
Find proteins for A0ACD6BAI3 (Planctomycetota bacterium) Explore A0ACD6BAI3  Go to UniProtKB:  A0ACD6BAI3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
crRNA	B	61	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
target RNA	C	25	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Nakagawa, R., Soumya, K., Han, A., Takeda, N.S., Tomita, A., Hirano, H., Kusakizako, T., Tomohiro, N., Yamashita, K., Feng, Z., 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: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2022-09-14
  Changes: Database references
• Version 1.2: 2024-06-26
  Changes: Data collection, Refinement description