9B0L

Cryo-EM structure of Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex

• PDB DOI: https://doi.org/10.2210/pdb9B0L/pdb
• NAKB: 9B0L
• EM Map EMD-44046: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA/RNA
• Organism(s): Acanthamoeba polyphaga mimivirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-12 Released: 2024-10-09 
• Deposition Author(s): Qayyum, M.Z., Schargel, R.D., Tanwar, A.S., Kellogg, E.H., Kalathur, R.C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Fanzor2 reveals insights into the evolution of the TnpB superfamily.

Schargel, R.D., Qayyum, M.Z., Tanwar, A.S., Kalathur, R.C., Kellogg, E.H.

(2024) Nat Struct Mol Biol 

• PubMed: 39354233 
• DOI: https://doi.org/10.1038/s41594-024-01394-4
• Primary Citation of Related Structures:  
  9B0L


• PubMed Abstract: 
  

  RNA-guided endonucleases, once thought to be exclusive to prokaryotes, have been recently identified in eukaryotes and are called Fanzors. They are classified into two clades, Fanzor1 and Fanzor2. Here we present the cryo-electron microscopy structure of Acanthamoeba polyphaga mimivirus Fanzor2, revealing its ωRNA architecture, active site and features involved in transposon-adjacent motif recognition. A comparison to Fanzor1 and TnpB structures highlights divergent evolutionary paths, advancing our understanding of RNA-guided endonucleases.

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Organizational Affiliation: 

Department of Microbiology, Cornell University, Ithaca, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 151.63 kDa 
• Atom Count: 7,051 
• Modelled Residue Count: 621 
• Deposited Residue Count: 805 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TnpB-like protein L79	B [auth P]	520	Acanthamoeba polyphaga mimivirus	Mutation(s): 0  Gene Names: MIMI_L79
UniProt
Find proteins for Q5UPF5 (Acanthamoeba polyphaga mimivirus) Explore Q5UPF5  Go to UniProtKB:  Q5UPF5

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3')	A [auth B]	11	Acanthamoeba polyphaga mimivirus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*CP*A)-3')	C [auth D]	4	Acanthamoeba polyphaga mimivirus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*GP*AP*GP*GP*TP*GP*GP*CP*TP*GP*CP*CP*CP*CP*GP*AP*CP*CP*GP*TP*C)-3')	D [auth A]	23	Acanthamoeba polyphaga mimivirus

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (117-MER)	E [auth C]	247	Acanthamoeba polyphaga mimivirus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	F [auth P]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	G [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Qayyum, M.Z., Schargel, R.D., Tanwar, A.S., Kellogg, E.H., Kalathur, R.C.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release