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- EMDB-52285: Structure of tRNA bound Ba1Cas12a3 -

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Basic information

Entry
Database: EMDB / ID: EMD-52285
TitleStructure of tRNA bound Ba1Cas12a3
Map data
Sample
  • Complex: tRNA bound Ba1Cas12a3
    • Protein or peptide: Ba1Cas12a3
    • RNA: crRNA
    • RNA: targetRNA
    • RNA: Ala tRNA
  • Ligand: MAGNESIUM ION
Keywordscrispar-cas nuclease / RNA BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesBacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria) / synthetic construct (others) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYuan B / Heinz DW
Funding support Germany, 1 items
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, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52285.png

Downloads & links

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Map

FileDownload / File: emd_52285.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.12244848 - 0.19937308
Average (Standard dev.)0.000035970308 (±0.0031485711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 327.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52285_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52285_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : tRNA bound Ba1Cas12a3

EntireName: tRNA bound Ba1Cas12a3
Components
  • Complex: tRNA bound Ba1Cas12a3
    • Protein or peptide: Ba1Cas12a3
    • RNA: crRNA
    • RNA: targetRNA
    • RNA: Ala tRNA
  • Ligand: MAGNESIUM ION

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Supramolecule #1: tRNA bound Ba1Cas12a3

SupramoleculeName: tRNA bound Ba1Cas12a3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Bacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)

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Macromolecule #1: Ba1Cas12a3

MacromoleculeName: Ba1Cas12a3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)
Molecular weightTheoretical: 135.303656 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: METYKVTKTI RFKLEAQNVP EIQKDIEGLQ SEFNLANFVS DLKNYLDQVR NYLFSEGKEH VFVNNKITIK REWLQNHAKQ EWVDFLEKN KRNNSLNNHT RRIQMSIGDF TGLASKIEGT FDEINSICKG LADAAGAQAN KRTKRERTGL LLKRLQARKA L PSLFSLIE ...String:
METYKVTKTI RFKLEAQNVP EIQKDIEGLQ SEFNLANFVS DLKNYLDQVR NYLFSEGKEH VFVNNKITIK REWLQNHAKQ EWVDFLEKN KRNNSLNNHT RRIQMSIGDF TGLASKIEGT FDEINSICKG LADAAGAQAN KRTKRERTGL LLKRLQARKA L PSLFSLIE NSADKNETGN LSLQLKNKSI LIEQQLAAGV QTFLPAQSGG LPVAKASFNY YTINKKPVDF GNEKSELESR LK ISIDTIF KLTRENFSKK IEEAITADIQ KELNNGKTLL LGDVPMLGIE NYVSLRQILK NIKSNQKKAF SDLMQSGKNY NEL KATNLY LLNTIEQRQF DNYKVKTNEL EKLAVKINQA TNDNQKKELI SNKQRVAKQR GIIMRDNFAT WKSFSNFYRT ISQE HGKIL ALLKGIEKER TESQLLKYWA LILENNGQHK LILIPREKAA SCKQWIASLN PSGDKLTKLF WFESLTYRSL QKLCF GFTE NGNNKFNKNI QNLLPKDNSR KIINGEFAFQ GDEQKKIKFY QSVLESKYAQ SVLNIPIQQV QADIINQSFA SLDDFQ IAL EKICYRLFAV VEANIEAELL KNDKAQIFNI TSSDLRKEAK DKIKSHTQIW KAFWTSENKQ NNFETRLNPE ITITYRQ PK QSKIDKYGER SQKNNRYLHA QYTLITTISE HSNSPTKILS FMSDDEFKSS VDTFNKKFKK DEIKFAFGID NGEVELST L GVYFPAFDKT TYKEKVAELE KVNDYGFEVL TIRNLNYKET DYNGKERKII QNPSYFLKKE NYLRTFNKSE TAYQKMFTE QFEKKKLLTL DLTTAKVICG HIVTNGDVPA LFNLWLKHAQ RNIFEMNDHI QKETAKKIVL KNQLDTDNEK LKFAEYISKE KEFGKLNDD EKMKYTKWIF EDRDQNNFTE VENKKFKRCQ KIYGNYSTKA KAPVLFASCF IDEELQSVTD IFDVRHIFKK R EDFYALKT EEEIKQLIDS YNTNRASHDI SNEELDLKIL NTKKALVANA VGVIDFLYKH YERRLGGEGL IIKEGFGTGK VE DGIEKFS GNIYRILERK LYQKFQNYGL VPPIKSLMAV RANGIENNKN AILQLGNVGF IDPAGTSQEC PVCIEGRLEH TTT CPNKCG FNSERIMHSN DGIASFNIAK RGFNNFVKSK TDKQLEHHHH HH

UniProtKB: UNIPROTKB: A0A2N2ZXC5

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Macromolecule #2: crRNA

MacromoleculeName: crRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.859344 KDa
SequenceString:
GUCUAAACCG ACCCAAUAAU UUCUACUGUU GUAGAUGAGG GAUCUCGCUC CUGGAAGAUG GUGAU

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Macromolecule #3: targetRNA

MacromoleculeName: targetRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.292981 KDa
SequenceString:
AAUCCCAUCA CCAUCUUCCA GGAGCGAGAU CCCUCCAAAA UC

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Macromolecule #4: Ala tRNA

MacromoleculeName: Ala tRNA / type: rna / ID: 4 / Details: tRNA (Ala) / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.476531 KDa
SequenceString:
GGGGCUAUAG CUCAGCUGGG AGAGCGCCUG CUUUGCACGC AGGAGGUCUG CGGUUCGAUC CCGCAUAGCU CCACCA

GENBANK: GENBANK: CP053605.1

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 50mM TrisHCl 50mM NaCl 1mM DTT 5% glycerol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116277
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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