8VZ6 | pdb_00008vz6

PbAbiF dimer bound to ncRNA

• PDB DOI: https://doi.org/10.2210/pdb8VZ6/pdb
• EM Map EMD-43682: EMDB EMDataResource
• NAKB: 8VZ6

• Classification: TOXIN/RNA
• Organism(s): uncultured Prevotellaceae bacterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-10 Released: 2025-02-12 
• Deposition Author(s): Wilkinson, M.E., Zilberzwige-Tal, S., Altae-Tran, H., Zhang, F.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.56 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins.

Zilberzwige-Tal, S., Altae-Tran, H., Kannan, S., Wilkinson, M.E., Vo, S.C., Strebinger, D., Edmonds, K.K., Yao, C.J., Mears, K.S., Shmakov, S.A., Makarova, K.S., Macrae, R.K., Koonin, E.V., Zhang, F.

(2025) Cell 188: 1925-1940.e20

• PubMed: 39970912 
• DOI: https://doi.org/10.1016/j.cell.2025.01.034
• Primary Citation Related Structures: 
  8VZ6


• PubMed 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 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.

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Organizational Affiliation: 
• Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Molecular Cellular Biology, Harvard University, Cambridge, MA, USA.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 101.93 kDa 
• Atom Count: 6,954 
• Modeled Residue Count: 692 
• Deposited Residue Count: 700 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Abi family protein	A, C [auth B]	300	uncultured Prevotellaceae bacterium	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
AbiF ncRNA	B [auth R], D [auth S]	50	uncultured Prevotellaceae bacterium

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.56 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Wilkinson, M.E., Zilberzwige-Tal, S., Altae-Tran, H., Zhang, F.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01HG009761

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2026-08-26
  Changes: Data collection, Database references