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- PDB-9b0l: Cryo-EM structure of Acanthamoeba polyphaga mimivirus Fanzor2 ter... -

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Basic information

Entry
Database: PDB / ID: 9b0l
TitleCryo-EM structure of Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
Components
  • 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')
  • DNA (5'-D(P*CP*CP*CP*A)-3')
  • DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3')
  • RNA (117-MER)
  • TnpB-like protein L79
KeywordsDNA BINDING PROTEIN/DNA/RNA / Transposon / Fanzor / cryo-EM / DNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


transposition / DNA recombination / DNA binding / metal ion binding
Similarity search - Function
: / Probable transposase, IS891/IS1136/IS1341 / Probable transposase / Transposase IS605, OrfB, C-terminal / Cas12f1-like, TNB domain
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / TnpB-like protein L79
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsQayyum, M.Z. / Schargel, R.D. / Tanwar, A.S. / Kellogg, E.H. / Kalathur, R.C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structure of Fanzor2 reveals insights into the evolution of the TnpB superfamily.
Authors: Richard D Schargel / M Zuhaib Qayyum / Ajay Singh Tanwar / Ravi C Kalathur / Elizabeth H Kellogg /
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. ...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.
History
DepositionMar 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 9, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 9, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 9, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 9, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 9, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 9, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Jun 4, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.2Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3')
P: TnpB-like protein L79
D: DNA (5'-D(P*CP*CP*CP*A)-3')
A: 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')
C: RNA (117-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6277
Polymers151,5385
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 3 types, 3 molecules BDA

#1: DNA chain DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3')


Mass: 3415.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acanthamoeba polyphaga mimivirus
#3: DNA chain DNA (5'-D(P*CP*CP*CP*A)-3')


Mass: 1135.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acanthamoeba polyphaga mimivirus
#4: DNA chain 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')


Mass: 7083.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acanthamoeba polyphaga mimivirus

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Protein / RNA chain , 2 types, 2 molecules PC

#2: Protein TnpB-like protein L79


Mass: 60572.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_L79 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UPF5
#5: RNA chain RNA (117-MER)


Mass: 79330.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Production host: Escherichia coli (E. coli) / References: GenBank: 55416625

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Acanthamoeba polyphaga mimivirus
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2250 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189912 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037501
ELECTRON MICROSCOPYf_angle_d0.52310829
ELECTRON MICROSCOPYf_dihedral_angle_d22.5992557
ELECTRON MICROSCOPYf_chiral_restr0.0361323
ELECTRON MICROSCOPYf_plane_restr0.003799

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