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- PDB-8vz6: PbAbiF dimer bound to ncRNA -

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Basic information

Entry
Database: PDB / ID: 8vz6
TitlePbAbiF dimer bound to ncRNA
Components
  • Abi family protein
  • AbiF ncRNA
KeywordsTOXIN/RNA / toxin-antitoxin / RNP / RNA-binding protein / HEPN / TOXIN / TOXIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesuncultured Prevotellaceae bacterium (environmental samples)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsWilkinson, M.E. / Zilberzwige-Tal, S. / Altae-Tran, H. / Zhang, F.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Aug 26, 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

Downloads & links

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Assembly

Deposited unit
A: Abi family protein
R: AbiF ncRNA
B: Abi family protein
S: AbiF ncRNA


Theoretical massNumber of molelcules
Total (without water)101,9264
Polymers101,9264
Non-polymers00
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 Abi family protein


Mass: 35008.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NCBI GCA_900316285.1 contig: ONCG01000034.1 start 16721 end 17623 strand +
Source: (gene. exp.) uncultured Prevotellaceae bacterium (environmental samples)
Production host: Escherichia coli (E. coli)
#2: RNA chain AbiF ncRNA


Mass: 15954.489 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NCBI GCA_900316285.1 contig: ONCG01000034.1 start 16721 end 17623 strand +
Source: (gene. exp.) uncultured Prevotellaceae bacterium (environmental samples)
Production host: Escherichia coli (E. coli)
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: AbiF RNP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)Organism: uncultured Prevotellaceae bacterium (environmental samples)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 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
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.69 sec. / Electron dose: 42.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4272
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7ISOLDEmodel fitting
8Cootmodel fitting
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1142600
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12790 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0067326
ELECTRON MICROSCOPYf_angle_d1.14210390
ELECTRON MICROSCOPYf_dihedral_angle_d16.611830
ELECTRON MICROSCOPYf_chiral_restr0.061230
ELECTRON MICROSCOPYf_plane_restr0.008954

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