9HLX | pdb_00009hlx

Structure of Ba1Cas12a3 binary complex

• PDB DOI: https://doi.org/10.2210/pdb9HLX/pdb
• EM Map EMD-52275: EMDB EMDataResource
• NAKB: 9HLX

• Classification: RNA BINDING PROTEIN
• Organism(s): Bacteroidota bacterium, synthetic construct
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-12-17 
• Deposition Author(s): Yuan, B., Heinz, D.W.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity.

Dmytrenko, O., Yuan, B., Crosby, K.T., Krebel, M., Chen, X., Nowak, J.S., Chramiec-Glabik, A., Filani, B., Gribling-Burrer, A.S., van der Toorn, W., von Kleist, M., Achmedov, T., Smyth, R.P., Glatt, S., Bravo, J.P.K., Heinz, D.W., Jackson, R.N., Beisel, C.L.

(2026) Nature 649: 1312-1321

• PubMed: 41501459 
• DOI: https://doi.org/10.1038/s41586-025-09852-9
• Primary Citation Related Structures: 
  9HLX, 9HM4, 9HM5, 9HM6


• PubMed Abstract: 
  

  In all domains of life, tRNAs mediate the transfer of genetic information from mRNAs to proteins. As their depletion suppresses translation and, consequently, viral replication, tRNAs represent long-standing and increasingly recognized targets of innate immunity ^1-5 . Here we report Cas12a3 effector nucleases from type V CRISPR-Cas adaptive immune systems in bacteria that preferentially cleave tRNAs after recognition of target RNA. Cas12a3 orthologues belong to one of two previously unreported nuclease clades that exhibit RNA-mediated cleavage of non-target RNA, and are distinct from all other known type V systems. Through cell-based and biochemical assays and direct RNA sequencing, we demonstrate that recognition of a complementary target RNA by the CRISPR RNA triggers Cas12a3 to cleave the conserved 5'-CCA-3' tail of diverse tRNAs to drive growth arrest and anti-phage defence. Cryogenic electron microscopy structures further revealed a distinct tRNA-loading domain that positions the tRNA tail in the RuvC active site of the nuclease. By designing synthetic reporters that mimic the tRNA acceptor stem and tail, we expanded the capacity of current CRISPR-based diagnostics for multiplexed RNA detection. Overall, these findings reveal widespread tRNA inactivation as a previously unrecognized CRISPR-based immune strategy that broadens the application space of the existing CRISPR toolbox.

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Organizational Affiliation: 
• Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA.
Malopolska Center of Biotechnology, Jagiellonian University, Krakow, Poland.
Architecture et Réactivitié de l'ARN, Université de Strasbourg, CNRS, Institute of Molecular and Cellular Biology (IBMC), University of Strasbourg, Strasbourg, France.
Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
Project Groups, Robert Koch Institute, Berlin, Germany.
University of Veterinary Medicine, Vienna, Austria.
Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany. [e-mail].
Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA. [e-mail].
Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. [e-mail].
Medical Faculty, University of Würzburg, Würzburg, Germany. [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: 156.16 kDa 
• Atom Count: 10,286 
• Modeled Residue Count: 1,197 
• Deposited Residue Count: 1,233 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ba1Cas12a3	A	1,168	Bacteroidota bacterium	Mutation(s): 0  Gene Names: CVT95_05895

Entity ID: 2
Molecule	Chains	Length	Organism	Image
crRNA	B	65	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Yuan, B., Heinz, D.W.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release
  
• Version 1.1: 2026-05-27
  Changes: Data collection, Database references