9B0L image
Deposition Date 2024-03-12
Release Date 2024-10-09
Last Version Date 2025-06-04
Entry Detail
PDB ID:
9B0L
Keywords:
DNA BINDING PROTEIN/DNA/RNA
Title:
Cryo-EM structure of Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
Biological Source:
Source Organism:
Acanthamoeba polyphaga mimivirus (Taxon ID: 212035)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.99 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9B0L validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule: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')
Chain IDs:D (auth: A)
Chain Length:23
Number of Molecules:1
Biological Source:Acanthamoeba polyphaga mimivirus
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3')
Chain IDs:A (auth: B)
Chain Length:11
Number of Molecules:1
Biological Source:Acanthamoeba polyphaga mimivirus
Polymer Type:polyribonucleotide
Molecule:RNA (117-MER)
Chain IDs:E (auth: C)
Chain Length:247
Number of Molecules:1
Biological Source:Acanthamoeba polyphaga mimivirus
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*CP*CP*CP*A)-3')
Chain IDs:C (auth: D)
Chain Length:4
Number of Molecules:1
Biological Source:Acanthamoeba polyphaga mimivirus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TnpB-like protein L79
Gene (Uniprot):MIMI_L79
Chain IDs:B (auth: P)
Chain Length:520
Number of Molecules:1
Biological Source:Acanthamoeba polyphaga mimivirus
UniProt ID:Q5UPF5 Pfam ID:PF01385, PF07282
Ligand Molecules
MG
ZN
Primary Citation
Structure of Fanzor2 reveals insights into the evolution of the TnpB superfamily.
Nat.Struct.Mol.Biol. 32 243 246 (2025)
PMID: 39354233 DOI: 10.1038/s41594-024-01394-4

Abstact

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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Primary Citation of related structures
9B0L