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- EMDB-66089: Cryo-EM strucutre of MbpAgo-gDNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-66089
TitleCryo-EM strucutre of MbpAgo-gDNA complex
Map dataMbpAgo-gDNA complex map
Sample
  • Complex: MbpAgo-gDNA complex
    • Protein or peptide: Piwi domain-containing protein
    • DNA: guide DNA (5'-D(P*T)-R(P*GP*AP*GP*G)-D(P*T)-R(P*AP*G)-3')
KeywordsMucilaginibacter paludis Argonaute with guide DNA / RNA BINDING PROTEIN/DNA / RNA BINDING PROTEIN-DNA complex
Function / homologyRibonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / Piwi domain-containing protein
Function and homology information
Biological speciesMucilaginibacter paludis DSM 18603 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsZhao X / Zhang K / Li S
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural and mechanistic insights into MbpAgo
Authors: Zhao X / Zhang K / Li S
History
DepositionSep 3, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66089.png

Downloads & links

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Map

FileDownload / File: emd_66089.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMbpAgo-gDNA complex map
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: 0.02
Minimum - Maximum-0.14467162 - 0.30766597
Average (Standard dev.)0.00042830958 (±0.008649462)
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: MbpAgo-gDNA complex map sharp

Fileemd_66089_additional_1.map
AnnotationMbpAgo-gDNA complex map_sharp
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: MbpAgo-gDNA complex map halfA

Fileemd_66089_half_map_1.map
AnnotationMbpAgo-gDNA complex map_halfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: MbpAgo-gDNA complex map halfB

Fileemd_66089_half_map_2.map
AnnotationMbpAgo-gDNA complex map_halfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MbpAgo-gDNA complex

EntireName: MbpAgo-gDNA complex
Components
  • Complex: MbpAgo-gDNA complex
    • Protein or peptide: Piwi domain-containing protein
    • DNA: guide DNA (5'-D(P*T)-R(P*GP*AP*GP*G)-D(P*T)-R(P*AP*G)-3')

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Supramolecule #1: MbpAgo-gDNA complex

SupramoleculeName: MbpAgo-gDNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mucilaginibacter paludis DSM 18603 (bacteria)

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Macromolecule #1: Piwi domain-containing protein

MacromoleculeName: Piwi domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mucilaginibacter paludis DSM 18603 (bacteria)
Molecular weightTheoretical: 93.827383 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSSGE NLYFQGMKDH ILNLYRIDNL SELDFSYKLI DFDLSFIAGK EELLNKQLQK IAEEVSSVTK GPTAVLKRNQ RFFVAVPAD KQMEDRSIDG IPFSIPIKLL PEVYRIDSKD IQGHQLDVVY KFLDYEIRRQ LGQHRDLWKL NTHQFFLREP M KGIQGSIN ...String:
HHHHHHSSGE NLYFQGMKDH ILNLYRIDNL SELDFSYKLI DFDLSFIAGK EELLNKQLQK IAEEVSSVTK GPTAVLKRNQ RFFVAVPAD KQMEDRSIDG IPFSIPIKLL PEVYRIDSKD IQGHQLDVVY KFLDYEIRRQ LGQHRDLWKL NTHQFFLREP M KGIQGSIN VFEGFTYKLA RLADGHFYVT LDLSTKYIDK YCLSHYINEG NVRTFENNYK GRRFLYLNGD NWYTIELLGF GK SVKEQDF IREGTTYNVL NYITEKIEHS RTDLKRYVKP NDLSMSYTYP GRTMDPHSGA TSLARMLYNT KDERVKSLHY LSI KGPSKR FEAINNYISS YFKNLKFNAG KLLISNEPLV EKIKNFWIPE LLFNNNRRLK ITGFNSGMRD FAYQRKQLIK NNGV LNRTS FDVQYLLVPD EQYMDANLVE GFKNNAEFLI KKLAPAFDKF IIIRYPVKSC TSASVQIQEI EKVLHRRNAL HGFAL VVLP DLDAFSPAFL KTFHELLKSK FYPDLKVQCA SAHNISSFFK PFSTAGNNGI VEYRVVEALK GRFSSYLFYL VLEHLI VNR KWPYALAKNL FYDIYIGIDV HDRHAGFTFF FKNGEQIIFH PEEVPQKTNS QRVEKVRAKT LNKVIYEKLK LYIPLFA PN PNGIVIVRDG RSFGVEYKAL QAAINTLAAE GIVNKDTVKY GVVDLHKQSS VPIRIAAKTN SYDQLENPVA GSYKLVSP K EGFIFSTGYP FDIKGTSRPL NLSMKEGDLD FMKVMEDVFC QIMLAFSAPD KSNFLPVIIK LIDTLLEPLT ATRETADEA EEDEEEMMDI N

UniProtKB: Piwi domain-containing protein

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Macromolecule #2: guide DNA (5'-D(P*T)-R(P*GP*AP*GP*G)-D(P*T)-R(P*AP*G)-3')

MacromoleculeName: guide DNA (5'-D(P*T)-R(P*GP*AP*GP*G)-D(P*T)-R(P*AP*G)-3')
type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.64166 KDa
SequenceString:
(DT)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DT)(DA) (DG)(DG)(DT)(DT)(DG)(DT)(DA)(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

Concentration0.33 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 325973
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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