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- EMDB-69324: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-69324
TitleCryo-EM structure of EcBPAN-guide RNA-target DNA complex
Map data
Sample
  • Complex: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex
    • RNA: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
    • DNA: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
    • Protein or peptide: EcbAgaN
    • Protein or peptide: EcAgo
  • Ligand: MAGNESIUM ION
KeywordsArgonaute proteins / nucleic acid binding / nuclease / defence system / DNA BINDING PROTEIN/DNA/RNA / DNA BINDING PROTEIN-DNA-RNA complex
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsLiu M / Yu Q / Shi DJ / Xing Q / Ma LX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex
Authors: Liu M / Yu Q / Shi DJ / Xing Q / Ma LX
History
DepositionFeb 23, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69324.png

Downloads & links

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Map

FileDownload / File: emd_69324.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 640 pix.
= 362.88 Å		0.57 Å/pix.
x 640 pix.
= 362.88 Å		0.57 Å/pix.
x 640 pix.
= 362.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.567 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02158
Minimum - Maximum-0.06191325 - 0.15512465
Average (Standard dev.)0.0007888502 (±0.007692362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 362.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_69324_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69324_half_map_2.map
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 EcBPAN-guide RNA-target DNA complex

EntireName: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex
Components
  • Complex: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex
    • RNA: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
    • DNA: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
    • Protein or peptide: EcbAgaN
    • Protein or peptide: EcAgo
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex

SupramoleculeName: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP...

MacromoleculeName: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
type: rna / ID: 1 / Number of copies: 8
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.697044 KDa
SequenceString:
AUCAAAGCUU AGAUACCCUG G

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

MacromoleculeName: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
type: dna / ID: 2 / Number of copies: 8 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.453182 KDa
SequenceString:
(DC)(DC)(DA)(DG)(DG)(DG)(DT)(DA)(DT)(DC) (DT)(DA)(DA)(DG)(DC)(DT)(DT)(DT)(DG)(DA) (DT)

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Macromolecule #3: EcbAgaN

MacromoleculeName: EcbAgaN / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 44.45773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVPIEKGNVY QLRDYFHSKV IESAHIDPFK SCFFSLLEGV KSCITNFSFA DLSLYQRCAI SGLGILDETV SVQDVSRLLG QAPKIDSTP RPWVSDMFGV MAVKWLTAQM QDESIDHEFE KWISGFLAQQ IESNHLSVFE KDIAAYVSNS ESASFSSACI P LFLHYRKL ...String:
MVPIEKGNVY QLRDYFHSKV IESAHIDPFK SCFFSLLEGV KSCITNFSFA DLSLYQRCAI SGLGILDETV SVQDVSRLLG QAPKIDSTP RPWVSDMFGV MAVKWLTAQM QDESIDHEFE KWISGFLAQQ IESNHLSVFE KDIAAYVSNS ESASFSSACI P LFLHYRKL LKINSHQDRL SLVGRFMSEF QAQATENPSV TLLCVMLYVF NQTNQEIAIA PPSGWTLDDL LGFLEHIPAG LK RWTWEDS GRTRGAEPVK WQVENEYHVQ NLLYILLAPI FNDIADEVNL QPVGQKNPRI DLYLPSLHTI IEVKYRKDTR KSF PLLIGE IAEDASLYRV DEKYKDSYII SFLWDCTRAT QEHVKFKEGV LKIKGIDGCV VISAPSTMSF KKKE

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Macromolecule #4: EcAgo

MacromoleculeName: EcAgo / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 82.492133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPIVLNAFPL KIPELELKFV QIPYDKTTLD SLRSSHKVTH VFRRQGDNIQ IFSSDGTFPK PGTPQTLQLK DNLGTFCSLV KDGLLKHFA GLGRTPCGFN PIEVVSAKPK DNLLASILGE AYPLKICAKY SIDTRTVQGQ PCLIIDCSTR RVVKENCLFF L KTGFNVIG ...String:
MPIVLNAFPL KIPELELKFV QIPYDKTTLD SLRSSHKVTH VFRRQGDNIQ IFSSDGTFPK PGTPQTLQLK DNLGTFCSLV KDGLLKHFA GLGRTPCGFN PIEVVSAKPK DNLLASILGE AYPLKICAKY SIDTRTVQGQ PCLIIDCSTR RVVKENCLFF L KTGFNVIG RYVVTEQDDG FRKLLGFVES CHEGRTLSVI RPDGQAVHAE AKDVYLEASR ANFDDYILHT HGTKKDSIVE HI RQSVSIF NGGENKKDRI DALKKYIQAT NISLLDGTRI EIEDPSDIQK DCAQMQKPVF VFNDNGEADW TEKGLTQNGP YTK RTFDRN DPSICVICAQ HDKGRVEQFV RKLLKGMANS KYFRNGLEGK FALGTSRVEV FETSTDSVDA YKNAIEAAIR KKAD DGGRW DLALVQVRQS FKKLKVADNP YYLGKSLFYL HQVPVQDFTI ELLTQSDYSL GYSLNNMSLA CYAKMGGVPW LLKSS PTLS HELVIGIGSA NIVQERGAHN QRIMGITTVF SGDGSYIVSS TSKAVVPEAY CDALTSVLAE NIEKIQRRMN WQKGDT IRL IFHVQVKKFN KEEIQAVRAV IDKYRDYQIE YAFVKISENH GLHMFDSSTA TMSKGRLATH RGKTFKLSKN EMLVYLI GQ RELRQETDGH PRGVIVNVHK DSTFKDIKYL SAQLYSFASH SWRSYFPNPM PVTITYSDLI AHNLGWLNQL PGWSDSVM I GKIGHSQWFL

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 309746
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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