[English] 日本語
Yorodumi
- EMDB-61487: Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric ternary... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61487
TitleCryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric ternary complex
Map dataCryo-EM structure of CpAgo_gDNA-tg_bubble dsDNA monomeric ternary complex
Sample
  • Complex: Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric 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 / 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: 3.2 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

-
Structure visualization

Supplemental images

emd_61487.png

Downloads & links

-
Map

FileDownload / File: emd_61487.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of CpAgo_gDNA-tg_bubble 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: 0.027
Minimum - Maximum-0.08367752 - 0.19693023
Average (Standard dev.)0.00017117755 (±0.005909533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

-
Supplemental data

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

Fileemd_61487_additional_1.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_bubble dsDNA monomeric ternary complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_61487_half_map_1.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_bubble dsDNA monomeric ternary complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_61487_half_map_2.map
AnnotationCryo-EM structure of CpAgo_gDNA-tg_bubble dsDNA monomeric ternary complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric ternary...

EntireName: Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric ternary complex
Components
  • Complex: Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric 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

-
Supramolecule #1: Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric ternary...

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

-
Macromolecule #1: Clostridium perfringen Argonaute

MacromoleculeName: Clostridium perfringen 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

-
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)

-
Macromolecule #3: DNA (58-MER)

MacromoleculeName: DNA (58-MER) / type: dna / ID: 3 / Number of copies: 1 / 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)

-
Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
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
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1609554
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 159745
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more