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

Emergence of a CRISPR RNA-guiding mechanism from a type III toxin-antitoxin system

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

To be published.

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