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- PDB-9hm4: Structure of tRNA bound Ba1Cas12a3 -

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Basic information

Entry
Database: PDB / ID: 9hm4
TitleStructure of tRNA bound Ba1Cas12a3
Components
  • Ala tRNA
  • Ba1Cas12a3
  • crRNA
  • targetRNA
KeywordsRNA BINDING PROTEIN / crispar-cas nuclease
Function / homology: / RNA / RNA (> 10) / :
Function and homology information
Biological speciesBacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)
Escherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYuan, B. / Heinz, D.W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: Nature / Year: 2026
Title: RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity.
Authors: Oleg Dmytrenko / Biao Yuan / Kadin T Crosby / Max Krebel / Xiye Chen / Jakub S Nowak / Andrzej Chramiec-Głąbik / Bamidele Filani / Anne-Sophie Gribling-Burrer / Wiep van der Toorn / Max ...Authors: Oleg Dmytrenko / Biao Yuan / Kadin T Crosby / Max Krebel / Xiye Chen / Jakub S Nowak / Andrzej Chramiec-Głąbik / Bamidele Filani / Anne-Sophie Gribling-Burrer / Wiep van der Toorn / Max von Kleist / Tatjana Achmedov / Redmond P Smyth / Sebastian Glatt / Jack P K Bravo / Dirk W Heinz / Ryan N Jackson / Chase L Beisel /
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- ...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. 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.
History
DepositionDec 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1May 27, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ba1Cas12a3
B: crRNA
C: targetRNA
D: Ala tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,9816
Polymers193,9334
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ba1Cas12a3


Mass: 135303.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)
Gene: CVT95_05895 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N2ZXC5
#2: RNA chain crRNA


Mass: 20859.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain targetRNA


Mass: 13292.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain Ala tRNA


Mass: 24476.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: tRNA (Ala) / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1845258627
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: tRNA bound Ba1Cas12a3 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Bacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5 / Details: 50mM TrisHCl 50mM NaCl 1mM DTT 5% glycerol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116277 / Symmetry type: POINT

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