8WF9 | pdb_00008wf9

Cryo-EM structure of the PspCas13b-crRNA-target RNA complex (State 1)

• PDB DOI: https://doi.org/10.2210/pdb8WF9/pdb
• NAKB: 8WF9
• EM Map EMD-37487: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Prevotella sp., synthetic construct
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 


• Deposited: 2023-09-19 Released: 2025-03-19 
• Deposition Author(s): Ishikawa, J., Kato, K., Yamashita, K., Nishizawa, T., Nishimasu, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.13 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into RNA-guided RNA editing by the Cas13b-ADAR2 complex.

Ishikawa, J., Kato, K., Kannan, S., Okazaki, S., Ishiguro, S., Yamashita, K., Yachie, N., Nishizawa, T., Zhang, F., Nishimasu, H.

(2025) Nat Struct Mol Biol 32: 1567-1578

• PubMed: 40217120 
• DOI: https://doi.org/10.1038/s41594-025-01529-1
• Primary Citation Related Structures: 
  8WF8, 8WF9, 8WFA, 8WFB


• PubMed Abstract: 
  

  Cas13 is an RNA-guided RNA endonuclease derived from the type VI CRISPR-Cas system, which has been used in numerous RNA-targeting technologies, such as RNA knockdown, detection and editing. The catalytically inactive Prevotella sp. Cas13b (dPspCas13b) fused to the human adenosine deaminase acting on RNA 2 (ADAR2) deaminase domain can edit adenosine in target transcripts to inosine, in an RNA-editing technology called REPAIR (RNA editing for programmable A-to-I replacement), which has potential for gene therapy. Here we report the cryo-electron microscopy structures of the PspCas13b-guide RNA binary complex, the PspCas13b-guide RNA-target RNA ternary complex and the dPspCas13b-ADAR2-guide RNA-target RNA complex. These structures provide mechanistic insights into RNA cleavage and editing. We applied our structural insights to engineer a compact and efficient dPspCas13b-ADAR2 complex (REPAIR-mini). Overall, our findings advance the understanding of CRISPR-Cas13 effector nucleases and could enable the development of improved RNA-targeting technologies.

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Organizational Affiliation: 
• Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
Department of Molecular and Mechanistic Immunology, Tokyo Medical and Dental University, Tokyo, Japan.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.
Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka, Japan.
Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
Howard Hughes Medical Institute, Cambridge, MA, USA.
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan. [e-mail].
Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan. [e-mail].
Inamori Research Institute for Science, Kyoto, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 160.8 kDa 
• Atom Count: 9,816 
• Modeled Residue Count: 1,074 
• Deposited Residue Count: 1,196 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PspCas13b	A	1,094	Prevotella sp.	Mutation(s): 0
UniProt
Find proteins for A0A926KZT7 (Streptomyces griseicoloratus) Explore A0A926KZT7  Go to UniProtKB:  A0A926KZT7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
crRNA	B	66	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
target RNA	C	36	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.13 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Ishikawa, J., Kato, K., Yamashita, K., Nishizawa, T., Nishimasu, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23KJ0720
Japan Agency for Medical Research and Development (AMED)	Japan	22am0401005h0004

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release
  
• Version 1.1: 2025-04-23
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-06-18
  Changes: Data collection
• Version 1.3: 2025-08-27
  Changes: Data collection, Database references