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- EMDB-55261: cryo-EM structure of LwHicAB-crRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-55261
Titlecryo-EM structure of LwHicAB-crRNA
Map data
Sample
  • Complex: LwHicAB-crRNA
    • Protein or peptide: Toxin-antitoxin system, antitoxin component, HicB family
    • Protein or peptide: Toxin-antitoxin system, toxin component, HicA family
    • RNA: RNA (58-MER)
Keywordstoxin-antitoxin / CRISPR RNA binding / prokaryotic immunity / IMMUNE SYSTEM
Function / homologyHicA mRNA interferase family / HicA superfamily / HicA toxin of bacterial toxin-antitoxin, / TTHA1013/TTHA0281-like / mRNA binding / Toxin-antitoxin system, toxin component, HicA family / Toxin-antitoxin system, antitoxin component, HicB family
Function and homology information
Biological speciesLeptotrichia wadei F0279 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiang L / Jiyun C / Xueyan L
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 937-2022European Union
CitationJournal: Nat Commun / Year: 2026
Title: Potential role of a CRISPR-Cas-activated toxin-antitoxin system in bacterial immunity.
Authors: Jiyun Chen / Linglong Huang / Hong Chen / Xueyan Li / Xiaofeng Lin / Chenmin Guo / Xi Liu / Guowei Fu / Ying Chen / Liang Liu /
Abstract: CRISPR-Cas and toxin-antitoxin systems can serve as antiviral defense mechanisms in prokaryotes. In typical toxin-antitoxin systems, toxin activation can limit phage propagation by inducing growth ...CRISPR-Cas and toxin-antitoxin systems can serve as antiviral defense mechanisms in prokaryotes. In typical toxin-antitoxin systems, toxin activation can limit phage propagation by inducing growth arrest or reduced cellular fitness, while the antitoxin neutralizes toxin activity. Here, we study potential functional synergy between a CRISPR-Cas13a system and a type II toxin-antitoxin module (HicAB) from a Leptotrichia bacterium, when heterologously expressed in E. coli, as well as in biochemical and structural analyses. We show that the antitoxin HicB exhibits toxic properties, and Cas13a directly activates HicB, triggering growth inhibition and conferring protection against bacteriophages. Structural analyses reveal that Cas13a binding promotes the spatial proximity of HicB tetramers, likely enabling its activation. The toxin HicA competitively binds to HicB, thereby inhibiting Cas13a-mediated HicB activation. Importantly, both CRISPR RNA and HicB independently suppress HicA toxicity. Structural evidence indicates that CRISPR RNA forms a hetero-tetradecameric complex with HicAB, occluding HicA's active site and neutralizing its toxic function. Thus, our findings indicate functional synergy between distinct bacterial immune strategies.
History
DepositionOct 3, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55261.png

Downloads & links

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Map

FileDownload / File: emd_55261.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 320 pix.
= 214.4 Å		0.67 Å/pix.
x 320 pix.
= 214.4 Å		0.67 Å/pix.
x 320 pix.
= 214.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.005064342 - 0.011683176
Average (Standard dev.)0.000025713858 (±0.00039991186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 214.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55261_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_55261_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : LwHicAB-crRNA

EntireName: LwHicAB-crRNA
Components
  • Complex: LwHicAB-crRNA
    • Protein or peptide: Toxin-antitoxin system, antitoxin component, HicB family
    • Protein or peptide: Toxin-antitoxin system, toxin component, HicA family
    • RNA: RNA (58-MER)

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Supramolecule #1: LwHicAB-crRNA

SupramoleculeName: LwHicAB-crRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leptotrichia wadei F0279 (bacteria)

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Macromolecule #1: Toxin-antitoxin system, antitoxin component, HicB family

MacromoleculeName: Toxin-antitoxin system, antitoxin component, HicB family
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Leptotrichia wadei F0279 (bacteria)
Molecular weightTheoretical: 15.86715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFYPAVVT KEDGTYYGCI VDFDKFEDGE INYYATFGNS MEEAVSNLRE TLGLHLADFL DVRKKFPEPS KVEDVKLKEN QYLYILSVD PVYEVAKVTN ALKKKTLTIP VWLDILAQEK NLNFSQILQK ALKKELGIE

UniProtKB: Toxin-antitoxin system, antitoxin component, HicB family

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Macromolecule #2: Toxin-antitoxin system, toxin component, HicA family

MacromoleculeName: Toxin-antitoxin system, toxin component, HicA family / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptotrichia wadei F0279 (bacteria)
Molecular weightTheoretical: 7.239685 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIFMSYRKIE KRFRKLGGKV VAIRGSHYQW MIPGVEGVVT VPYSKDIPVG TLRSIEKQVG IKF

UniProtKB: Toxin-antitoxin system, toxin component, HicA family

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Macromolecule #3: RNA (58-MER)

MacromoleculeName: RNA (58-MER) / type: rna / ID: 3 / Number of copies: 2
Source (natural)Organism: Leptotrichia wadei F0279 (bacteria)
Molecular weightTheoretical: 18.564164 KDa
SequenceString:
GAGCACCCCA AAAAUGAAGG GGACUAAAAC ACAAAUCUAU CUGAAUAAAC UCUUCUUC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration3.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
100.0 mMNaClsodium chloride
1.0 mMC4H10O2S2DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 120000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1184599
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9svk:
cryo-EM structure of LwHicAB-crRNA

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