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- EMDB-43682: PbAbiF dimer bound to ncRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-43682
TitlePbAbiF dimer bound to ncRNA
Map dataSharpened map of PbAbiF (C2 symmetry)
Sample
  • Complex: AbiF RNP
    • Protein or peptide: Abi family protein
    • RNA: AbiF ncRNA
Keywordstoxin-antitoxin / RNP / RNA-binding protein / HEPN / TOXIN / TOXIN-RNA complex
Biological speciesuncultured Prevotellaceae bacterium (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsWilkinson ME / Zilberzwige-Tal S / Altae-Tran H / Zhang F
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01HG009761 United States
CitationJournal: Cell / Year: 2025
Title: Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins.
Authors: Shai Zilberzwige-Tal / Han Altae-Tran / Soumya Kannan / Max E Wilkinson / Samuel Chau-Duy-Tam Vo / Daniel Strebinger / KeHuan K Edmonds / Chun-Chen Jerry Yao / Kepler S Mears / Sergey A ...Authors: Shai Zilberzwige-Tal / Han Altae-Tran / Soumya Kannan / Max E Wilkinson / Samuel Chau-Duy-Tam Vo / Daniel Strebinger / KeHuan K Edmonds / Chun-Chen Jerry Yao / Kepler S Mears / Sergey A Shmakov / Kira S Makarova / Rhiannon K Macrae / Eugene V Koonin / Feng Zhang /
Abstract: Despite ongoing efforts to study CRISPR systems, the evolutionary origins giving rise to reprogrammable RNA-guided mechanisms remain poorly understood. Here, we describe an integrated ...Despite ongoing efforts to study CRISPR systems, the evolutionary origins giving rise to reprogrammable RNA-guided mechanisms remain poorly understood. Here, we describe an integrated sequence/structure evolutionary tracing approach to identify the ancestors of the RNA-targeting CRISPR-Cas13 system. We find that Cas13 likely evolved from AbiF, which is encoded by an abortive infection-linked gene that is stably associated with a conserved non-coding RNA (ncRNA). We further characterize a miniature Cas13, classified here as Cas13e, which serves as an evolutionary intermediate between AbiF and other known Cas13s. Despite this relationship, we show that their functions substantially differ. Whereas Cas13e is an RNA-guided RNA-targeting system, AbiF is a toxin-antitoxin (TA) system with an RNA antitoxin. We solve the structure of AbiF using cryoelectron microscopy (cryo-EM), revealing basic structural alterations that set Cas13s apart from AbiF. Finally, we map the key structural changes that enabled a non-guided TA system to evolve into an RNA-guided CRISPR system.
History
DepositionFeb 10, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43682.png

Downloads & links

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Map

FileDownload / File: emd_43682.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of PbAbiF (C2 symmetry)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 240 pix.
= 238.68 Å		0.99 Å/pix.
x 240 pix.
= 238.68 Å		0.99 Å/pix.
x 240 pix.
= 238.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9945 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.050837386 - 0.09070917
Average (Standard dev.)0.000029140598 (±0.0036831172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 238.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43682_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PbAbiF refinement, half-map 1

Fileemd_43682_half_map_1.map
AnnotationPbAbiF refinement, half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PbAbiF refinement, half-map 2

Fileemd_43682_half_map_2.map
AnnotationPbAbiF refinement, half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AbiF RNP

EntireName: AbiF RNP
Components
  • Complex: AbiF RNP
    • Protein or peptide: Abi family protein
    • RNA: AbiF ncRNA

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Supramolecule #1: AbiF RNP

SupramoleculeName: AbiF RNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: uncultured Prevotellaceae bacterium (environmental samples)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Abi family protein

MacromoleculeName: Abi family protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: uncultured Prevotellaceae bacterium (environmental samples)
Molecular weightTheoretical: 35.008711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNRIPFPKP YTSAHDLVSL LQSRGLTIAD TAKTERYLEF IGYYRLSAYM YPLLQMPKEQ HRYKPNTTFD QVMMLYRFDK KLRLLIFNE IEKIEVAVRS AIVNIGSDMI GSPFWMTDGS NFIDPRKFRH TMDLIDAELG RSREDFIVHF KQTYSDAYPP A WILAEVLP ...String:
MSNRIPFPKP YTSAHDLVSL LQSRGLTIAD TAKTERYLEF IGYYRLSAYM YPLLQMPKEQ HRYKPNTTFD QVMMLYRFDK KLRLLIFNE IEKIEVAVRS AIVNIGSDMI GSPFWMTDGS NFIDPRKFRH TMDLIDAELG RSREDFIVHF KQTYSDAYPP A WILAEVLP FGVITNIFSN IKTARIKKSI ARKFGLQVAP FESWLTIVAL TRNSCCHHAR VWNKQNTIRP MIPNRMTGRW II LPTDALR IYFNLCIIKY FLDIISPQND MKAKIDALLS SYSSIDINAM GFPRGWESEP LWQ

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Macromolecule #2: AbiF ncRNA

MacromoleculeName: AbiF ncRNA / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: uncultured Prevotellaceae bacterium (environmental samples)
Molecular weightTheoretical: 15.954489 KDa
SequenceString:
ACUAGAACCC GCCAAGCCUC UCAACGAUGC UCAAAUGUGC GGGUCGUUUU

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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

Concentration2 mg/mL
BufferpH: 7.9
Details: 10 mM HEPES-KOH pH 7.9, 250 mM potassium acetate, 2.5 mM magnesium acetate, 5 mM beta-mercaptoethanol, 5 mM desthiobiotin
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4272 / Average exposure time: 0.69 sec. / Average electron dose: 42.2 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: 3.2 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1142600
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 12790
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 36000 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8vz6:
PbAbiF dimer bound to ncRNA

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