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- EMDB-44046: Cryo-EM structure of Acanthamoeba polyphaga mimivirus Fanzor2 ter... -

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Basic information

Entry
Database: EMDB / ID: EMD-44046
TitleCryo-EM structure of Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
Map data
Sample
  • Complex: Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
    • DNA: DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3')
    • Protein or peptide: TnpB-like protein L79
    • DNA: DNA (5'-D(P*CP*CP*CP*A)-3')
    • DNA: 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')
    • RNA: RNA (117-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsTransposon / 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 / Putative transposase DNA-binding domain
Similarity search - Domain/homology
TnpB-like protein L79
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsQayyum MZ / Schargel RD / Tanwar AS / Kellogg EH / Kalathur RC
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Struct Mol Biol / Year: 2024
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, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44046.png

Downloads & links

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Map

FileDownload / File: emd_44046.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 360 pix.
= 375.84 Å		1.04 Å/pix.
x 360 pix.
= 375.84 Å		1.04 Å/pix.
x 360 pix.
= 375.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.044 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.6152247 - 2.911052
Average (Standard dev.)0.0005367135 (±0.02487788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 375.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44046_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44046_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex

EntireName: Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
Components
  • Complex: Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
    • DNA: DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3')
    • Protein or peptide: TnpB-like protein L79
    • DNA: DNA (5'-D(P*CP*CP*CP*A)-3')
    • DNA: 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')
    • RNA: RNA (117-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex

SupramoleculeName: Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Acanthamoeba polyphaga mimivirus

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

MacromoleculeName: DNA (5'-D(P*GP*AP*CP*GP*GP*TP*CP*GP*GP*GP*C)-3') / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Acanthamoeba polyphaga mimivirus
Molecular weightTheoretical: 3.415222 KDa
SequenceString:
(DG)(DA)(DC)(DG)(DG)(DT)(DC)(DG)(DG)(DG) (DC)

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Macromolecule #3: DNA (5'-D(P*CP*CP*CP*A)-3')

MacromoleculeName: DNA (5'-D(P*CP*CP*CP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Acanthamoeba polyphaga mimivirus
Molecular weightTheoretical: 1.135795 KDa
SequenceString:
(DC)(DC)(DC)(DA)

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Macromolecule #4: DNA (5'-D(P*AP*GP*GP*AP*GP*GP*TP*GP*GP*CP*TP*GP*CP*CP*CP*CP*GP*AP...

MacromoleculeName: 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')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Acanthamoeba polyphaga mimivirus
Molecular weightTheoretical: 7.083547 KDa
SequenceString:
(DA)(DG)(DG)(DA)(DG)(DG)(DT)(DG)(DG)(DC) (DT)(DG)(DC)(DC)(DC)(DC)(DG)(DA)(DC)(DC) (DG)(DT)(DC)

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Macromolecule #2: TnpB-like protein L79

MacromoleculeName: TnpB-like protein L79 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba polyphaga mimivirus
Molecular weightTheoretical: 60.572387 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEAVKNVKP KVPAKKRIIT GSKTKKKVFV KKKPPDKKPL KKPVKKTVKT DKPKSIYVPN KDLKISKWIP TPKKEFTEIE TNSWYEHRK FENPNKSPVQ TYNKIVPVVP PESIKQQNLA NKRKKTNRPI VFISSEKIRI YPTKDQQKIL QTWFRLFAYM Y NCTIDYIN ...String:
MKEAVKNVKP KVPAKKRIIT GSKTKKKVFV KKKPPDKKPL KKPVKKTVKT DKPKSIYVPN KDLKISKWIP TPKKEFTEIE TNSWYEHRK FENPNKSPVQ TYNKIVPVVP PESIKQQNLA NKRKKTNRPI VFISSEKIRI YPTKDQQKIL QTWFRLFAYM Y NCTIDYIN SKKVVLESGR INVAATRKVC NKISVRKAQK TIRDNLIQST NPSIMTHIID EAIGLACSNY KTCLTNYIER HI KKFDIKP WNMSKRKKII IIEANFFKKG TFCPTVFPKM ESSKPLTMID KTVTLQYDSD TRKYILFVPR VTPKYSVNKE KNS CGIDPG LRDFLTVYSE NETQSICPIE IVVNTTKNEY KKIDKINEII KTKPNLNSKR KKKLNRGLRK YHRRVTNKMK DMHY KVSHE LVNTFDKICI GKLNVKSILS KANTVLKSAL KRKLATLSFY RFTQRLTHMG YKYGTEVVNV NEYLTTKTCS NCGKI KDLG ASKIYECESC GMYADRDENA AKNILKVGLK PWYKQK

UniProtKB: TnpB-like protein L79

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Macromolecule #5: RNA (117-MER)

MacromoleculeName: RNA (117-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Acanthamoeba polyphaga mimivirus
Molecular weightTheoretical: 79.330805 KDa
SequenceString: AAAAAUAGUC UAAUAAAAUC AGGGGUACAU UCCGCUAGUA CUCCACCCUA CGGGUUAAGC AAAUGAGAAU AUCGAAACGG UAUGCACAG GAUUCUUCGA GUGAUAAUCU UAGGAUGACU CACUAAGGAG AUGACUAAAG UGUAUCAUUC AAUAUUGUAU U GAACGGUA ...String:
AAAAAUAGUC UAAUAAAAUC AGGGGUACAU UCCGCUAGUA CUCCACCCUA CGGGUUAAGC AAAUGAGAAU AUCGAAACGG UAUGCACAG GAUUCUUCGA GUGAUAAUCU UAGGAUGACU CACUAAGGAG AUGACUAAAG UGUAUCAUUC AAUAUUGUAU U GAACGGUA UUCUUCCAUA GAGAGUUGAU UUUUGGAGUA UCCAAAAAUA UCAACUUUUU AUGAGCGGGC AGCCACCUCC UU GUUAUUG

GENBANK: GENBANK: AY653733.1

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 189912
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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