9B0L | pdb_00009b0l

Cryo-EM structure of Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

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.

(2025) Nat Struct Mol Biol 32: 243-246

  • DOI: https://doi.org/10.1038/s41594-024-01394-4
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Department of Microbiology, Cornell University, Ithaca, NY, USA. rds278@cornell.edu.

Macromolecule Content 

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

Macromolecules


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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TnpB-like protein L79B [auth P]520Acanthamoeba polyphaga mimivirusMutation(s): 0 
Gene Names: MIMI_L79
UniProt
Find proteins for Q5UPF5 (Acanthamoeba polyphaga mimivirus)
Explore Q5UPF5 
Go to UniProtKB:  Q5UPF5
Entity Groups
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UniProt GroupQ5UPF5
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3')A [auth B]11Acanthamoeba polyphaga mimivirus
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*CP*A)-3')C [auth D]4Acanthamoeba polyphaga mimivirus
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
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]23Acanthamoeba polyphaga mimivirus
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (117-MER)E [auth C]247Acanthamoeba polyphaga mimivirus
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-04
    Changes: Data collection