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- EMDB-61474: Cryo-EM structure of CpAgo in complex with the 5'-P guide DNA. -

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Basic information

Entry
Database: EMDB / ID: EMD-61474
TitleCryo-EM structure of CpAgo in complex with the 5'-P guide DNA.
Map datacryo-EM structure of CpAgo-gDNA binary complex
Sample
  • Complex: Cryo-EM structure of CpAgo in complex with the 5'-P guide DNA.
    • Protein or peptide: Clostridium perfringens Argonaute (CpAgo)
    • 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')
KeywordspAgos / nucleotide-binding pocket / PAZ / cryo-EM / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Biological speciesClostridium perfringens (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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 9, 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_61474.png

Downloads & links

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Map

FileDownload / File: emd_61474.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM structure of CpAgo-gDNA binary 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: 0.08
Minimum - Maximum-0.11467015 - 0.29250193
Average (Standard dev.)-0.00034620054 (±0.010469872)
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 binary complex

Fileemd_61474_additional_1.map
Annotationcryo-EM structure of CpAgo-gDNA binary 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 binary complex

Fileemd_61474_half_map_1.map
Annotationcryo-EM structure of CpAgo-gDNA binary 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 binary complex

Fileemd_61474_half_map_2.map
Annotationcryo-EM structure of CpAgo-gDNA binary 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 in complex with the 5'-P guide DNA.

EntireName: Cryo-EM structure of CpAgo in complex with the 5'-P guide DNA.
Components
  • Complex: Cryo-EM structure of CpAgo in complex with the 5'-P guide DNA.
    • Protein or peptide: Clostridium perfringens Argonaute (CpAgo)
    • 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')

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Supramolecule #1: Cryo-EM structure of CpAgo in complex with the 5'-P guide DNA.

SupramoleculeName: Cryo-EM structure of CpAgo in complex with the 5'-P guide DNA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 90 KDa

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Macromolecule #1: Clostridium perfringens Argonaute (CpAgo)

MacromoleculeName: Clostridium perfringens Argonaute (CpAgo) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 86.32925 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 DGFSREDLDW 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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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: 47.6 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
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3428472
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 1373978
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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