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- EMDB-61485: Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61485
TitleCryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex
Map dataCryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex
Sample
  • Complex: Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex
    • Protein or peptide: Clostridium perfringens 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 (29-MER)
  • Ligand: MANGANESE (II) ION
KeywordspAgos / 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: 3.42 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_61485.png

Downloads & links

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Map

FileDownload / File: emd_61485.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 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: 0.097
Minimum - Maximum-0.13491134 - 0.30841285
Average (Standard dev.)-0.0003349671 (±0.011980534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 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 dsDNA monomeric ternary complex

Fileemd_61485_additional_1.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric 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 dsDNA monomeric ternary complex

Fileemd_61485_half_map_1.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric 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 dsDNA monomeric ternary complex

Fileemd_61485_half_map_2.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric 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 : Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex

EntireName: Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex
Components
  • Complex: Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex
    • Protein or peptide: Clostridium perfringens 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 (29-MER)
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex

SupramoleculeName: Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Clostridium perfringens Argonaute

MacromoleculeName: Clostridium perfringens Argonaute / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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: 1 / 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 (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.764712 KDa
SequenceString:
(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)

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 1 / 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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.064 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
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8586596
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 626358
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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