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- EMDB-61488: Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary c... -

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Basic information

Entry
Database: EMDB / ID: EMD-61488
TitleCryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
Map dataCryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
Sample
  • Complex: CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
    • Protein or peptide: Clostridium perfringen Argonaute
    • DNA: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
    • DNA: DNA (58-MER)
  • Ligand: MANGANESE (II) ION
KeywordspAgos / dimerization / nucleotide-binding pocket / PAZ / cryo-EM / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Biological speciesClostridium perfringens (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiu Y / Li S / Zhang K
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Dimeric state and novel nucleotide-binding pocket drive CpAgo-mediated DNA cleavage
Authors: Liu Y / Li S / Zhang K
History
DepositionSep 10, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61488.png

Downloads & links

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Map

FileDownload / File: emd_61488.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.11713005 - 0.25228354
Average (Standard dev.)0.00022195163 (±0.006984943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM structure of CpAgo gDNA-tg bubble dsDNA dimeric ternary complex...

Fileemd_61488_additional_1.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of CpAgo gDNA-tg bubble dsDNA dimeric ternary complex...

Fileemd_61488_half_map_1.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of CpAgo gDNA-tg bubble dsDNA dimeric ternary complex...

Fileemd_61488_half_map_2.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex

EntireName: CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
Components
  • Complex: CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
    • Protein or peptide: Clostridium perfringen Argonaute
    • DNA: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
    • DNA: DNA (58-MER)
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex

SupramoleculeName: CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Clostridium perfringen Argonaute

MacromoleculeName: Clostridium perfringen Argonaute / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 86.285242 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVGGYKVSNL TVEAFEGIGS VNPMLFYQYK VTGKGKYDNV YKIIKSARYK MHSKNRFKPV FIKDDKLYTL EKLPDIEDLD FANINFVKS EVLSIEDNMS IYGEVVEYYI NLKLKKVKVL GKYPKYRINY SKEILSNTLL TRELKDEFKK SNKGFNLKRK F RISPVVNK ...String:
MVGGYKVSNL TVEAFEGIGS VNPMLFYQYK VTGKGKYDNV YKIIKSARYK MHSKNRFKPV FIKDDKLYTL EKLPDIEDLD FANINFVKS EVLSIEDNMS IYGEVVEYYI NLKLKKVKVL GKYPKYRINY SKEILSNTLL TRELKDEFKK SNKGFNLKRK F RISPVVNK MGKVILYLSC SADFSTNKNI YEMLKEGLEV EGLAVKSEWS NISGNLVIES VLETKISEPT SLGQSLIDYY KN NNQGYRV KDFTDEDLNA NIVNVRGNKK IYMYIPHALK PIITREYLAK NDPEFSKEIE QLIKMNMNYR YETLKSFVND IGV IEELNN LSFKNKYYED VKLLGYSSGK IDEPVLMGAK GIIKNKMQIF SNGFYKLPEG KVRFGVLYPK EFDGVSRKAI RAIY DFSKE GKYHGESNKY IAEHLINVEF NPKECIFEGY ELGDITEYKK AALKLNNYNN VDFVIAIVPN MSDEEIENSY NPFKK IWAE LNLPSQMISV KTAEIFANSR DNTALYYLHN IVLGILGKIG GIPWVVKDMK GDVDCFVGLD VGTREKGIHY PACSVV FDK YGKLINYYKP NIPQNGEKIN TEILQEIFDK VLISYEEENG AYPKNIVIHR AGFSREDLDW YENYFGKKNI KFNIIEV KK STPLKIASIN EGNITNPEKG SYILRGNKAY MVTTDIKENL GSPKPLKIEK SYGDIDMLTA LSQIYALTQI HVGATKSL R LPITTGYADK ICKAIEFIPQ GRVDNRLFFL

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Macromolecule #2: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP...

MacromoleculeName: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.588266 KDa
SequenceString:
(DT)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DT)(DA) (DG)(DG)(DT)(DT)(DG)(DT)(DA)(DT)(DA)(DG) (DT)

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Macromolecule #3: DNA (58-MER)

MacromoleculeName: DNA (58-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.721516 KDa
SequenceString: (DA)(DT)(DT)(DT)(DA)(DA)(DA)(DT)(DA)(DA) (DT)(DT)(DT)(DA)(DA)(DT)(DA)(DT)(DA)(DC) (DT)(DA)(DT)(DA)(DC)(DA)(DA)(DC)(DC) (DT)(DA)(DC)(DT)(DA)(DC)(DC)(DT)(DC)(DA) (DT) (DA)(DT)(DA)(DA)(DA)(DT) ...String:
(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DT)(DA)(DA) (DT)(DT)(DT)(DA)(DA)(DT)(DA)(DT)(DA)(DC) (DT)(DA)(DT)(DA)(DC)(DA)(DA)(DC)(DC) (DT)(DA)(DC)(DT)(DA)(DC)(DC)(DT)(DC)(DA) (DT) (DA)(DT)(DA)(DA)(DA)(DT)(DT)(DT) (DT)(DT)(DA)(DA)(DA)(DT)(DA)(DA)(DA)(DT)

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1609554
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 50418
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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