9MVR | pdb_00009mvr

AI-designed Cas13 anti-CRISPR AIcrVIA1

• PDB DOI: https://doi.org/10.2210/pdb9MVR/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

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: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.43 kDa 
• Atom Count: 1,341 
• Modeled Residue Count: 154 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.403	α = 90
b = 62.9	β = 90
c = 84.927	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Taveneau, C., Chai, H.X., 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: Database references