9MVS | pdb_00009mvs

Activated Leptotrichia buccalis (Lbu) CRISPR-Cas13a bound to AI-designed anti-CRISPR AIcrVIA1

• PDB DOI: https://doi.org/10.2210/pdb9MVS/pdb
• NAKB: 9MVS
• EM Map EMD-48668: EMDB EMDataResource

• Classification: DE NOVO PROTEIN/HYDROLASE/RNA
• Organism(s): synthetic construct, Leptotrichia buccalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-15 Released: 2026-02-25 
• Deposition Author(s): Taveneau, C., Knott, G.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

De novo design of potent CRISPR-Cas13 inhibitors.

Taveneau, C., Chai, H.X., D'Silva, J., Bamert, R.S., Chen, H., Hayes, B.K., Calvert, R.W., Purcell, J., Curwen, D.J., Munder, F., Martin, L.L., Barr, J.J., Rosenbluh, J., Fareh, M., Grinter, R., Knott, G.J.

(2026) Nat Chem Biol 

• PubMed: 41588195 
• DOI: https://doi.org/10.1038/s41589-025-02136-3
• Primary Citation Related Structures: 
  9MVR, 9MVS


• PubMed Abstract: 
  

  CRISPR-Cas systems are transformative tools for gene editing that can be tuned or controlled by anti-CRISPRs (Acrs)-phage-derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that can inhibit biotechnologically relevant CRISPR systems are relatively rare and challenging to discover. To overcome this limitation, we describe a highly successful and rapid approach that leverages de novo protein design to develop new-to-nature proteins for controlling CRISPR-Cas activity. Here, using Leptotrichia buccalis CRISPR-Cas13a as a representative example, we demonstrate that Acrs designed using artificial intelligence (AIcrs) are capable of highly potent and specific inhibition of CRISPR-Cas13a nuclease activity. We present a comprehensive workflow for design validation and demonstrate AIcr functionality in controlling CRISPR-Cas13 activity in bacterial and human cells. The ability to design bespoke inhibitors of Cas effectors will contribute to the ongoing development of CRISPR-Cas tools in diverse applications across research, medicine, agriculture and microbiology.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
AI Protein Design Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
School of Chemistry, Monash University, Clayton, Victoria, Australia.
Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
Functional Genomics Platform, Monash University, Melbourne, Victoria, Australia.
AI Protein Design Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia. [e-mail].
Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia. [e-mail].
Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
AI Protein Design Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 174.95 kDa 
• Atom Count: 11,346 
• Modeled Residue Count: 1,261 
• Deposited Residue Count: 1,327 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AIcrVIA1	A [auth B]	83	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endoribonuclease Cas13a	B [auth A]	1,162	Leptotrichia buccalis	Mutation(s): 0  Gene Names: cas13a, c2c2, Lebu_1799 EC: 3.1
UniProt
Find proteins for C7NBY4 (Leptotrichia buccalis (strain ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b)) Explore C7NBY4  Go to UniProtKB:  C7NBY4

Entity ID: 3
Molecule	Chains	Length	Organism	Image
crRNA	C	56	Leptotrichia buccalis

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Guide complementary activator RNA (aRNA)	D	26	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Coot	0.9.4
RECONSTRUCTION	PHENIX	1.18.2
MODEL REFINEMENT	PHENIX	1.18.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Taveneau, C., Knott, G.J.

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Funding Organization	Location	Grant Number
Other private	Australia	SMRF2021-276

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release
  
• Version 1.1: 2026-04-29
  Changes: Data collection, Database references